Attenuated FNR Deficient Enterobacteria

ABSTRACT

The invention provides an attenuated enterobacterium comprising an attenuating mutation in the fnr gene, and optionally further comprising a heterologous nucleic acid encoding a foreign antigen. Also provided are pharmaceutical formulations comprising the attenuated enterobacteria of the invention. Further disclosed are methods of inducing an immune response in a subject by administration of an immunogenically effective amount of an attenuated enterobacterium or pharmaceutical formulation of the invention.

CROSS REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Provisional Application No. 60/831,821, filed Jul. 19, 2006, the disclosure of which is incorporated by reference herein in its entirety.

FIELD OF THE INVENTION

This invention relates to attenuated Fumarate-Nitrate Reductase (FNR) enterobacteria strains. In particular, this invention relates to attenuated FNR enterobacteria strains and methods of using the same to induce an immune response.

BACKGROUND OF THE INVENTION

Salmonella enterica serovar Typhimurium is a gram-negative facultative intracellular pathogen. Serovar Typhimurium infections usually result from ingestion of contaminated food or water. The organism generally targets and colonizes the intestinal epithelium of the host and causes gastroenteritis (i.e., salmonellosis). During a Salmonella infection, the growth phase and growth conditions of the organism are important in attachment, invasion, and the regulation of many of the virulence genes. Cells grown under limited oxygen concentrations are more invasive and adhere better to mammalian cells than do aerobically grown or stationary-phase cells. Salmonella invasion genes have been identified and localized. During infection, serovar Typhimurium must adapt to changes in [O₂] encountered in the gastrointestinal tract of the host. In Escherichia coli, transitions from aerobic to anaerobic environments or vice versa, involve changes in a large number of genes. However, upon sudden reappearance of oxygen, these cellular processes must be reversed in a precise and orderly fashion to ensure the safe transition to the oxygenated environment. This complex regulatory system has been extensively studied in E. coli, where the DNA-binding protein FNR encoded by fnr, senses changes in [O₂] and controls the expression of the different genes either alone or in cooperation with other regulators, e.g., ArcA.

SUMMARY OF THE INVENTION

The present invention is based, in part, on the inventors' discovery that enterobacteria comprising an attenuating mutation in the fnr (Fumarate-Nitrate Reductase) gene have an avirulent (i.e., highly attenuated) phenotype. Thus, the present invention provides attenuated enterobacteria and methods of using the same as attenuated immunogenic compositions, attenuated vaccines and/or as attenuated vaccine vectors to induce an immune response against a heterologous antigen in a subject.

Accordingly, a first aspect of the invention provides a pharmaceutical composition comprising an attenuated enterobacterium comprising an attenuating mutation (e.g., deletion) in the fnr gene in a pharmaceutically acceptable carrier.

A further aspect of the invention provides an attenuated enterobacterium comprising an attenuating mutation (e.g., a deletion) in the fnr gene and, optionally, further comprising a heterologous nucleic acid sequence encoding a foreign antigen. In particular embodiments, the attenuated enterobacterium is present in a pharmaceutical composition in a pharmaceutically acceptable carrier.

A further aspect of the present invention is a method of inducing an immune response in a subject comprising administering to the subject an immunogenically effective amount of an attenuated enterobacterium comprising an attenuating mutation (e.g., a deletion) in the fnr gene. In embodiments of the invention, the attenuated enterobacterium is provided in a pharmaceutical composition further comprising a pharmaceutically acceptable carrier. In further embodiments of the invention, the attenuated enterobacterium comprises a heterologous nucleic acid encoding a foreign antigen.

The invention further provides for the use of an attenuated enterobacterium or pharmaceutical composition of the invention to induce an immune response in a subject.

These and other aspects of the invention are set forth in more detail in the following description of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the location of the tnpA insertion (between bp 106 and 107) in the fnr gene. WT fnr sequences are in bold, and the sequences of the beginning and ending junctions of the tnpA insert are in italics. Arrows indicate the direction of transcription. IGS, intergenic spacer region. (Complete DNA sequences [i.e., ogt, tnpA/fnr junctions, and ydaA] are available at GenBank accession number AH015911.)

FIG. 2 shows a logo graph of the information matrix obtained from the consensus alignment of FNR motif sequences for serovar Typhimurium (derived from the corresponding FNR-regulated genes in E. coli). The total height of each column of characters represents the amount of information for that specific position, and the height of each character represents the frequency of each nucleotide.

FIG. 3 shows the correlation between the microarray and qRT-PCR data for 19 selected genes. The ratios of changes in gene expression, from the microarray and qRT-PCR experiments, for the FNR mutant relative to the WT were log₂ transformed and linearly correlated.

FIG. 4 shows a scheme representing the structural organization of the major genes involved in virulence/SPI-1 (A), ethanolamine utilization (B), and flagellar biosynthesis and motility/swarming (C to E). The names of genes are listed to the right of the arrows, an asterisk next to the gene indicates the presence of at least one FNR motif in the 5′ region, and the numbers to the left of the arrows indicate the ratio of gene expression in the fnr mutant relative to that in the WT.

FIG. 5 shows a comparison of the fnr mutant and the WT strain for virulence in 6- to 8-week-old C57BL/6 mice. (A) Groups of 10 mice were inoculated p.o. with 5×10⁶ and 5×10⁷ CFU/mouse. (B) Groups of five mice were challenged i.p. with 250 CFU/mouse, as described. Percent survival is the number of mice surviving relative to the number of mice challenged at time zero.

FIG. 6 shows a comparison of the WT, the fnr mutant, and the mutant strain harboring pfnr for survival inside peritoneal macrophages from C57BL/6 mice. The macrophages were harvested and treated as described. (A) Comparison between the fnr mutant and the WT strain. The number of viable cells found inside the macrophages, at time zero, following the removal of extracellular bacteria by washing/gentamicin treatment is defined as 100% survival. (B) Comparison between the WT, the fnr mutant, and the pfnr-complemented mutant. The number of viable cells found inside macrophages at 20 h is expressed as percent survival relative to that found inside macrophages at 2 h.

FIG. 7 shows the virulence of the WT and the fnr mutant in C57BL/6 mice and congenic gp91phox^(−/−) mice and survival of the bacteria inside peritoneal macrophages. The mice were challenged i.p. with 250 CFU/mouse, as described. (A) C57BL/6 and gp91phox^(−/−) mice treated with the WT strain. (B) C57BL/6 and gp91phox^(−/−) mice treated with the fnr mutant. (C) Survival of the WT and the fnr mutant inside macrophages from C57BL/6 and gp91phox^(−/−) mice. The number of viable cells at 20 h is expressed as percent survival relative to that found inside the macrophages at time zero.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is explained in greater detail below. This description is not intended to be a detailed catalog of all the different ways in which the invention may be implemented, or all the features that may be added to the instant invention. For example, features illustrated with respect to one embodiment may be incorporated into other embodiments, and features illustrated with respect to a particular embodiment may be deleted from that embodiment. In addition, numerous variations and additions to the various embodiments suggested herein will be apparent to those skilled in the art in light of the instant disclosure, which do not depart from the instant invention. Hence, the following specification is intended to illustrate some particular embodiments of the invention, and not to exhaustively specify all permutations, combinations, and variations thereof.

All publications, patents, and patent publications cited herein are incorporated by reference in their entireties for the teachings relevant to the sentence and/or paragraph in which the citation is presented.

As used herein, “a,” “an” or “the” can mean one or more than one. For example, “a” mutation can mean a single mutation or a multiplicity of mutations.

As used herein, “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (“or”).

FNR (Fumarate-Nitrate Reductase) is a DNA-binding regulator protein expressed by all enterobacteria including Salmonella spp., Escherichia spp., and Shigella spp. The fnr gene was previously known as oxrA in Salmonella spp. The present inventors have identified FNR as a global regulatory protein for the expression of virulent genes in enterobacteria. An FNR deleted (Δfnr) strain of a known virulent strain of S. enterica serovar Typhimurium was shown to be non-motile, lacking flagella, and having an avirulent phenotype. Thus, the present invention provides FNR deficient (e.g., Δfnr or fnr mutants) strains of enterobacteria that can be used to study the fnr gene, its role in virulence in these organisms, and can further be used as attenuated immunogenic compositions, attenuated vaccines (e.g., live attenuated vaccines) and/or attenuated vaccine vectors.

Enterobacteria are known in the art and are generally pathogens that can infect the gastrointestinal tract of avians and/or mammals. The present invention can be practiced with any suitable enterobacterium in the order Enterobacteriales and optionally in the family Enterobacteriaceae that encodes FNR, including but not limited to bacteria classified in the following genera: Alishewanella, Alterococcus, Aquamonas, Aranicola, Arsenophonus, Azotivirga, Blochmannia, Brenneria, Buchnera, Budvicia, Buttiauxella, Candidatus, Cedecea, Citrobacter, Dickeya, Edwardsiella, Enterobacter, Erwinia (e.g., E. amylovora), Escherichia, Ewingella, Grimontella, Hafnia, Klebsiella (e.g., K. pneumoniae), Kuyvera, Leclercia, Leminorella, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Candidatus Phlomobacter, Photohabdus, Plesiomonas (e.g., P. shigelloides), Pragia, Proteus (e.g., P. vulgaris), Providencia, Rahnella, Raoultella, Salmonella, Samsonia, Serratia (e.g., S. marcenscens), Shigella, Sodalis, Tatumella, Travulsiella, Wigglesworthia, Xenorhabdus, Yersinia (e.g., Y. pestis), and Yokenella.

In particular embodiments, the enterobacterium is a Salmonella spp., an Escherichia spp., or a Shigella spp.

Further, the enterobacterium can optionally be a pathogenic enterobacterium. In particular embodiments, the enterobacterium from which the FNR deficient strain is derived is a pathogenic (e.g., virulent) bacterium as that term is understood in the art, where the attenuating fnr mutation results in a reduction in the pathogenicity. In representative embodiments, the FNR deficient strain is highly attenuated so as to be avirulent (e.g., induces no or insignificant levels of pathogenicity).

The term “pathogenic” is understood in the art, for example, as causing pathogenicity such as morbidity and/or mortality in a subject or population of subjects.

The term “attenuating” with respect to pathogenic microorganisms is understood in the art, for example, as a reduction in pathogenicity (including no detectable pathogenicity) produced in the subject as a result of administration of the FNR deficient enterobacterium strain as compared with the level of pathogenicity produced if an enterobacterium with a fully functional fnr gene (e.g., the wild-type strain) were administered.

Methods of assessing pathogenicity of enterobacteria, and attenuation thereof, are known in the art (e.g., morbidity and/or mortality following challenge in a suitable animal model such as mice or survival in cultured macrophages).

Suitable Salmonella species within the scope of the present invention include but are not limited to S. bongori and S. enterica as well as S. enterica subspecies (e.g., enterica, salamae, arizonae, diarizonae, houtenae and indica). Numerous serovars of S. bongori and S. enterica are known and are within the scope of the present invention. Exemplary S. enterica serovars include Typhimurium, Typhi and Enteritidis.

The present invention can further be practiced with any species of Escherichia including but not limited to E. adecarboxylata, E. albertii, E. blattae, E. coli (including toxigenic strains such as E. coli O157:H7), E. fergusonii, E. hermannii, and E. vulneris.

Suitable species of Shigella include without limitation species in Serogroup A (e.g., S. dysenteriae and serotypes thereof), species in Serogroup B (e.g., S. flexneri and serotypes thereof), species in Serogroup C (e.g., S. boydii and serotypes thereof), and species in Serogroup D (e.g., S. sonnei and serotypes thereof).

The genomic sequences of numerous enterobacteria are known in the art. See, e.g., NCBI Accession No. NC_(—)004337 (Shigella flexneri 2a str. 301); NCBI Accession No. NC_(—)007613 (Shigella boydii Sb227); NCBI Accession No. AP009048 (E. coli W3110); NCBI Accession No. BA000007 (E. coli O157:H7 str. Sakai); NCBI Accession No. AE009952 (Y. pestis KIM); NCBI Accession No. NC_(—)003197 (S. typhimurium LT2); and NCBI Accession No. NC_(—)003198 (S. enterica subsp. enterica serovar Typhi str. CT18).

Likewise, the nucleic acid and amino acid sequences of the fnr gene from various enterobacteria are known in the art.

The attenuated enterobacteria of the present invention comprise an attenuating mutation in the fnr gene. In representative embodiments, the mutation is an attenuating deletion mutation (including truncations) that results in attenuation of the pathogenicity of the bacterium. Other mutations include without limitation attenuating insertions, substitutions and/or frame-shift mutations that result in attenuation of the pathogenicity of the bacterium. In embodiments of the invention, the mutation is a non-polar alteration in the fnr gene.

Deletion and insertion mutations can be any deletion/insertion mutation in the fnr gene that results in attenuation of the pathogenicity of the bacterium. In representative embodiments, the alteration is a deletion or an insertion of at least about 9, 30, 50, 75, 90, 120, 150, 180, 240, 300, 450 or more consecutive nucleotides in the fnr gene that results in attenuation of the pathogenicity of the bacterium. Optionally, essentially all (e.g., at least about 95%, 97%, 98% or more) or all of the fnr coding sequence is deleted. In other embodiments, essentially all or all of the fnr gene, including regulatory elements, is deleted. In particular embodiments, the deletion can extend beyond the fnr gene. Generally, however, the deletion does not render genes essential for growth, multiplication and/or survival non-functional. In particular embodiments, the deletion does not extend into any genes essential for growth, multiplication and/or survival. In embodiments of the invention, the deletion does not extend to genes that are 5′ and/or 3′ of the fnr coding region or the fnr gene.

One FNR deficient strain of S. enterica serovar Typhimurium has been constructed by the inventors and is shown in the Examples.

The FNR deficient enterobacterium strains of the invention can further comprise other mutations, including other attenuating mutations.

Generally, the FNR deficient enterobacterium strains will retain other appropriate genomic sequences to be able to grow, multiply and survive (e.g., in the gut of a host). Thus, the fnr mutations of the invention exclude lethal mutations that unduly inhibit the survival of the organism.

In embodiments of the invention, the FNR mutation results in at least about a 25%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 98% or more reduction in FNR mRNA, protein and/or activity. Methods of assessing levels of mRNA and proteins levels and FNR activity are known in the art.

The fnr mutation can be combined with any other mutation known in the art, including other attenuating mutations. For example, the fnr mutant enterobacterium can also comprise an arcA mutation. The ArcA protein cooperates with FNR for controlling the transitions from aerobic/anaerobic conditions and vice versa.

The attenuated enterobacteria of the present invention can be used as an attenuated immunogenic compositions or attenuated vaccine against enterobacteria (e.g., a live attenuated vaccine). Enterobacteria are described above. In embodiments of the invention, the enterobacterium is a pathogenic enterobacterium. For example, in particular embodiments, the invention provides live immunogenic compositions or live attenuated vaccines against Salmonella, Shigella or Escherichia. The attenuated enterobacterium vaccine can be used to induce an immune response against one species or against multiple closely related species/genera of enterobacteria (e.g., that cross-react with antibodies produced in response to administration of the attenuated enterobacterium).

Further, the attenuated FNR deficient enterobacterium strains of the invention can be used as vectors, e.g., to deliver an antigen(s) that is heterologous (e.g., foreign) to the enterobacterium vector (including any plasmids carried by the enterobacterium) to induce an immune response against other organisms (e.g., pathogenic organisms). In one embodiment, a heterologous nucleic acid sequence encoding the foreign antigen(s) is incorporated into the genomic DNA of the enterobacterium (e.g., inserted into or in place of a deleted fnr gene). In other embodiments, the heterologous nucleic acid sequence encoding the foreign antigen is incorporated into a plasmid that is carried by an attenuated FNR deficient host (e.g., a Δfnr host). Plasmids that are compatible with the various enterobacteria are known in the art.

The attenuated FNR deficient strains can further be used as vectors to deliver therapeutic proteins and untranslated RNAs (e.g., siRNA, shRNA, antisense RNA).

Methods of expressing foreign antigens in enterobacteria are known to those skilled in the art. For example, the foreign antigen can be expressed as part of a fusion with one of the structural proteins of the bacterial host (e.g., expressed on the surface of the bacterium) such as a flagellin protein (see, e.g., Chauhan et al., (2005) Molecular and Cellular Biochemistry 276:1-6) or a membrane protein as known in the art. See also, Chinchilla et al., (2007) Infection Immun. 75: 3769. In other embodiments, the foreign antigen is not expressed as a fusion with a host structural protein. According to this embodiment, the heterologous nucleic acid encoding the foreign antigen can optionally be operably associated with a leader sequence directing secretion of the foreign antigen from the bacterial cell.

The heterologous nucleic acid sequence encoding the foreign antigen can be operatively associated with any suitable promoter or other regulatory sequence. The promoter or regulatory sequence can be native or foreign to the host, can be native or foreign to the heterologous nucleic acid, and can further be partially or completely synthetic.

The codon usage of the heterologous nucleic acid sequence can be optimized for expression in the enterobacterium using methods known to those skilled in the art (see, e.g., Chinchilla et al., (2007) Infection Immun. 75: 3769.

The foreign antigen can be any suitable antigen known in the art, and can further be from a bacterial, yeast, fungal, protozoan or viral source. Suitable antigens include, but are not limited to antigens from pathogenic infectious agents.

The antigen can be an antigen from a pathogenic microorganism, which includes but is not limited to, Rickettsia, Chlamydia, Mycobacteria, Clostridia, Corynebacteria, Mycoplasma, Ureaplasma, Legionella, Shigella, Salmonella, pathogenic Escherichia coli species, Bordatella, Neisseria, Treponema, Bacillus, Haemophilus, Moraxella, Vibrio, Staphylococcus spp., Streptococcus spp., Campylobacter spp., Borrelia spp., Leptospira spp., Erlichia spp., Klebsiella spp., Pseudomonas spp., Helicobacter spp., and any other pathogenic microorganism now known or later identified (see, e.g., Microbiology, Davis et al, Eds., 4^(th) ed., Lippincott, New York, 1990, the entire contents of which are incorporated herein by reference for the teachings of pathogenic microorganisms).

Specific examples of microorganisms from which the antigen can be obtained include, but are not limited to, Helicobacter pylori, Chlamydia pneumoniae, Chlamydia trachomatis, Ureaplasma urealyticum, Mycoplasma pneumoniae, Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcus viridans, Enterococcus faecalis, Neisseria meningitidis, Neisseria gonorrhoeae, Treponema pallidum, Bacillus anthracis, Salmonella typhi, Vibrio cholera, Pasteurella pestis, Pseudomonas aeruginosa, Campylobacter jejuni, Clostridium difficile, Clostridium tetani, Clostridium botulinum, Mycobacterium tuberculosis, Borrelia burgdorferi, Haemophilus ducreyi, Corynebacterium diphtheria, Bordetella pertussis, Bordetella parapertussis, Bordetella bronchiseptica, Haemophilus influenza, and enterotoxic Escherichia coli.

The antigen can further be an antigen from a pathogenic protozoa, including, but not limited to, Plasmodium spp. (e.g., malaria antigens), Babeosis spp., Schistosoma spp., Trypanosoma spp., Pneumocystis carnii, Toxoplasma spp., Leishmania spp., and any other protozoan pathogen now known or later identified.

The antigen can also be an antigen from pathogenic yeast and fungi, including, but not limited to, Aspergillus spp., Candida spp., Cryptococcus spp., Histoplasma spp., Coccidioides spp., and any other pathogenic fungus now known or later identified.

Suitable antigens can include, but are not limited to, viral antigens such as antigens including but not limited to human hepatitis C virus (HCV) antigens and influenza antigens.

Other specific examples of various antigens include, but are not limited to, the B1 protein of hepatitis C virus (Bruna-Romero et al. (1997) Hepatology 25: 470-477), amino acids 252-260 of the circumsporozoite protein of Plasmodium berghei [Allsopp et al. (1996) Eur. J. Immunol. 26: 1951-1958], the influenza A virus nucleoprotein [e.g., residues 366-374; Nomura et al. (1996) J. Immunol. Methods 193: 4149], the listeriolysin O protein of Listeria monocytogenes [residues 91-99; An et al. (1996) Infect. Immun. 64: 1685-1693 ], P. falciparum antigens (causing malaria, e.g., tCSP), hepatitis B surface antigen [Gilbert et al. (1997) Nature Biotech. 15: 1280-1283], and E coli O157.H1.

The term “antigen” as used herein includes toxins such as the neurotoxin tetanospasmin produced by Clostridium tetani and the toxin produced by E. coli O157:H7.

In particular embodiments, the attenuated enterobacteria of the invention express a foreign antigen(s) and can be used to induce an immune response against both the enterobacterium and the organism(s) from which the foreign antigen(s) is derived and, optionally, other species/genera closely related to either of the foregoing (e.g., that cross-react with antibodies produced in response to administration of the attenuated enterobacterium).

There is no particular size limitation to the heterologous nucleic acid encoding the foreign antigen. When incorporated into the genomic DNA, the heterologous nucleic acid will generally be at least about 30, 50, 75, 100, 150 or 200 nucleotides in length and/or less than about 1, 1.5, 2, 2.5 or 3 kilobases in length. When carried by a plasmid, the heterologous nucleic acid can generally be longer, e.g., at least about 30, 50, 75, 100, 150, 200, 500 or 1000 nucleotides in length and/or less than about 5, 10, 12, 14, 16, 18 or 20 kilobases in length.

In representative embodiments, the FNR deficient enterobacterium is a Δfnr mutant, which advantageously reduces the probability of reversion to the wild-type pathogenic phenotype. For example, most current live attenuated vaccine strains against typhoid are auxotrophs for some nutrients, which are likely less stable than the deletion mutants.

The present invention can be used for therapeutic/prophylactic and non-therapeutic/prophylactic purposes. For example, the present invention provides FNR deficient (e.g., Δfnr) enterobacteria strains that can be used to study the fnr gene, its role in virulence in these organisms, and as attenuated immunogenic compositions, attenuated vaccines (e.g., live attenuated vaccines) and attenuated vaccine vectors (e.g., live attenuated vaccine vectors).

With respect to uses as an attenuated vaccine or vaccine vector, the present invention finds use in both veterinary and medical applications. Suitable subjects include avians, mammals and fish, with mammals being preferred. The term “avian” as used herein includes, but is not limited to, chickens, ducks, geese, quail, turkeys and pheasants. The term “mammal” as used herein includes, but is not limited to, primates (e.g., simians and humans), bovines, ovines, caprines, porcines, equines, felines, canines, lagomorphs, rodents (e.g., rats and mice), etc. Human subjects include fetal, neonatal, infant, juvenile and adult subjects.

The invention can be used in a therapeutic and/or prophylactic manner. For example, in one embodiment, to protect against an infectious disease, subjects may be vaccinated prior to exposure, e.g., as neonates or adolescents. Adults that have not previously been exposed to the disease may also be vaccinated.

In particular embodiments, the present invention provides a pharmaceutical composition comprising a FNR deficient (e.g., Δfnr) strain enterobacterium (optionally, a live FNR deficient enterobacterium) in a pharmaceutically-acceptable carrier, which can also include other medicinal agents, pharmaceutical agents, carriers, adjuvants, diluents, etc. For injection, the carrier is typically a liquid. For other methods of administration, the carrier may be either solid or liquid, such as sterile, pyrogen-free water or sterile pyrogen-free phosphate-buffered saline solution. For inhalation administration, the carrier will be respirable, and is optionally in solid or liquid particulate form. Formulation of pharmaceutical compositions is well known in the pharmaceutical arts [see, e.g., Remington's Pharmaceutical Sciences, 15th Edition, Mack Publishing Company, Easton, Pa. (1975)].

By “pharmaceutically acceptable” it is meant a material that is not biologically or otherwise undesirable, e.g., the material may be administered to a subject without causing undesirable biological effects.

The FNR deficient strains of the invention can be administered to elicit an immune response. Typically, immunological compositions of the present invention comprise an immunogenically effective amount of the FNR deficient strain enterobacterium as disclosed herein, optionally in combination with a pharmaceutically acceptable carrier.

An “immunogenically effective amount” is an amount that is sufficient to induce an immune response in the subject to which the composition is administered. Nonlimiting examples of dosages include about 10⁴ to 10⁹ colony forming units (cfu), about 10⁵ to 10⁸ cfu or about 10⁶ to 10⁷ cfu. Optionally, one or more booster dosages (e.g., about 10³ to 10⁸ cfu or 10⁴ to 10⁵ cfu) can be administered.

The invention also encompasses methods of producing an immune response in a subject, the method comprising: administering a FNR deficient (e.g., Δfnr) enterobacterium strain of the invention or a pharmaceutical formulation containing the same to a subject in an immunogenically effective amount so that an immune response is produced in the subject.

The terms “vaccination” or “immunization” are well-understood in the art. For example, the terms vaccination or immunization can be understood to be a process that increases a subject's immune reaction to antigen and thereby enhance the ability to resist and/or overcome infection.

Any suitable method of producing an immune response (e.g., immunization) known in the art can be employed in carrying out the present invention, as long as an active immune response (preferably, a protective immune response) is elicited.

In representative embodiments, less pathogenicity (including no detectable pathogenicity) is produced in the subject as a result of administration of the FNR deficient enterobacterium strain as compared with pathogenicity produced if an enterobacterium with a fully functional fnr gene (e.g., the wild-type strain) were administered (e.g., at least about a 25%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 98% or more reduction in pathogenicity).

Vaccines can be given as a single dose schedule or in a multiple dose schedule. A multiple dose schedule is one in which a primary course of administration may consist of about 1 to 10 separate doses, followed by other doses (i.e., booster doses) given at subsequent time intervals to maintain and/or reinforce the immune response, for example, at about 1 to 4 months for a second dose, and if needed, a subsequent dose(s) after another several months or year. The dosage regimen will also, at least in part, be determined by the need of the individual and be dependent upon the judgment of the medical or veterinary practitioner.

An “active immune response” or “active immunity” is characterized by “participation of host tissues and cells after an encounter with the immunogen. It involves differentiation and proliferation of immunocompetent cells in lymphoreticular tissues, which lead to synthesis of antibody or the development of cell-mediated reactivity, or both.” Herbert B. Herscowitz, Immunophysiology: Cell Function and Cellular Interactions in Antibody Formation, in IMMUNOLOGY: BASIC PROCESSES 117 (Joseph A. Bellanti ed., 1985). Alternatively stated, an active immune response is mounted by the host after exposure to immunogen by infection or by vaccination. Active immunity can be contrasted with passive immunity, which is acquired through the “transfer of preformed substances (antibody, transfer factor, thymic graft, interleukin-2) from an actively immunized host to a non-immune host.” Id.

A “protective” immune response or “protective” immunity as used herein indicates that the immune response confers some benefit to the subject in that it prevents or reduces the incidence of disease, the progression of the disease and/or the symptoms of the disease. Alternatively, a protective immune response or protective immunity may be useful in the treatment of disease including infectious disease. The protective effects may be complete or partial, as long as the benefits of the treatment outweigh any disadvantages thereof.

Administration of the attenuated enterobacteria and compositions of the invention can be by any means known in the art, including oral, rectal, topical, buccal (e.g., sub-lingual), vaginal, intra-ocular, parenteral (e.g., subcutaneous, intramuscular including skeletal muscle, cardiac muscle, diaphragm muscle and smooth muscle, intradermal, intravenous, intraperitoneal), topical (e.g., mucosal surfaces including airway surfaces), intranasal, transmucosal, intratracheal, transdermal, intraventricular, intraarticular, intrathecal and inhalation administration.

The most suitable route in any given case will depend on the nature and severity of the condition being treated, the FNR deficient strain enterobacterium, and the composition being administered.

The FNR deficient enterobacterium strain can be formulated for administration in a pharmaceutical carrier in accordance with known techniques. See, e.g., Remington, The Science and Practice of Pharmacy (9th Ed. 1995). In the manufacture of a pharmaceutical formulation according to the invention, the FNR deficient enterobacterium strain is typically admixed with, inter alia, an acceptable carrier. The carrier can be a solid or a liquid, or both, and is optionally formulated as a unit-dose formulation, which can be prepared by any of the well-known techniques of pharmacy.

For injection, the carrier is typically a liquid, such as sterile pyrogen-free water, pyrogen-free phosphate-buffered saline solution, bacteriostatic water, or Cremophor EL[R] (BASF, Parsippany, N.J.). For other methods of administration, the carrier can be either solid or liquid.

For oral administration, the FNR deficient enterobacterium strain can be administered in solid dosage forms, such as capsules, tablets, and powders, or in liquid dosage forms, such as elixirs, syrups, and suspensions. The FNR deficient strain enterobacterium can be encapsulated in gelatin capsules together with inactive ingredients and powdered carriers, such as glucose, lactose, sucrose, mannitol, starch, cellulose or cellulose derivatives, magnesium stearate, stearic acid, sodium saccharin, talcum, magnesium carbonate and the like. Examples of additional inactive ingredients that can be added to provide desirable color, taste, stability, buffering capacity, dispersion or other known desirable features are red iron oxide, silica gel, sodium lauryl sulfate, titanium dioxide, edible white ink and the like. Similar diluents can be used to make compressed tablets. Both tablets and capsules can be manufactured as sustained release products to provide for continuous release of medication over a period of hours. Compressed tablets can be sugar coated or film coated to mask any unpleasant taste and protect the tablet from the atmosphere, or enteric-coated for selective disintegration in the gastrointestinal tract. Liquid dosage forms for oral administration can contain coloring and flavoring to increase patient acceptance.

Formulations suitable for buccal (sub-lingual) administration include lozenges comprising the FNR deficient enterobacterium strain in a flavored base, usually sucrose and acacia or tragacanth; and pastilles comprising the FNR deficient enterobacterium strain in an inert base such as gelatin and glycerin or sucrose and acacia.

Formulations of the present invention suitable for parenteral administration can comprise sterile aqueous and non-aqueous injection solutions of the FNR deficient enterobacterium strain, which preparations are generally isotonic with the blood of the intended recipient. These preparations can contain anti-oxidants, buffers, bacteriostats and solutes, which render the formulation isotonic with the blood of the intended recipient. Aqueous and non-aqueous sterile suspensions can include suspending agents and thickening agents. The formulations can be presented in unit\dose or multi-dose containers, for example sealed ampoules and vials, and can be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example, saline or water-for-injection immediately prior to use.

Extemporaneous injection solutions and suspensions can be prepared from sterile powders, granules and tablets. For example, in one aspect of the present invention, there is provided an injectable, stable, sterile composition comprising a FNR deficient enterobacterium strain of the invention, in a unit dosage form in a sealed container. Optionally, the composition is provided in the form of a lyophilizate, which is capable of being reconstituted with a suitable pharmaceutically acceptable carrier to form a liquid composition suitable for injection thereof into a subject.

Formulations suitable for rectal or vaginal administration can be presented as suppositories. These can be prepared by admixing the FNR deficient enterobacterium strain with one or more conventional excipients or carriers, for example, cocoa butter, polyethylene glycol or a suppository wax, which are solid at room temperature, but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the FNR deficient FNR deficient enterobacterium strain.

Formulations suitable for topical application to the skin can take the form of an ointment, cream, lotion, paste, gel, spray, aerosol, or oil. Carriers that can be used include petroleum jelly, lanoline, polyethylene glycols, alcohols, transdermal enhancers, and combinations of two or more thereof.

Formulations suitable for transdermal administration can be presented as discrete patches adapted to remain in intimate contact with the epidermis of the recipient for a prolonged period of time. Formulations suitable for transdermal administration can also be delivered by iontophoresis [see, for example, Pharmaceutical Research 3 (6):318 (1986)] and typically take the form of an optionally buffered aqueous solution. Suitable formulations comprise citrate or bis\tris buffer (pH 6) or ethanol/water.

The FNR deficient enterobacterium strain can be formulated for nasal administration or otherwise administered to the lungs of a subject by any suitable means, for example, by an aerosol suspension of respirable particles comprising the FNR deficient enterobacterium strain, which the subject inhales. The respirable particles can be liquid or solid. The term “aerosol” includes any gas-borne suspended phase, which is capable of being inhaled into the bronchioles or nasal passages. Specifically, an aerosol includes a gas-borne suspension of droplets, as can be produced in a metered dose inhaler or nebulizer, or in a mist sprayer. An aerosol also includes a dry powder composition suspended in air or other carrier gas, which can be delivered by insufflation from an inhaler device, for example. See Ganderton & Jones, Drug Delivery to the Respiratory Tract, Ellis Horwood (1987); Gonda (1990) Critical Reviews in Therapeutic Drug Carrier Systems 6:273-313; and Raeburn et al. (1992) J. Pharmacol. Toxicol. Methods 27:143-159. Aerosols of liquid particles can be produced by any suitable means, such as with a pressure-driven aerosol nebulizer or an ultrasonic nebulizer, as is known to those of skill in the art. See, e.g., U.S. Pat. No. 4,501,729. Aerosols of solid particles comprising the FNR deficient enterobacterium strain can likewise be produced with any solid particulate medicament aerosol generator, by techniques known in the pharmaceutical art.

In particular embodiments of the invention, administration is by subcutaneous or intradermal administration. Subcutaneous and intradermal administration can be by any method known in the art, including but not limited to injection, gene gun, powderject device, bioject device, microenhancer array, microneedles, and scarification (i.e., abrading the surface and then applying a solution comprising the FNR deficient enterobacterium strain).

In other embodiments, the FNR deficient enterobacterium strain is administered intramuscularly, for example, by intramuscular injection.

The examples which follow are set forth to illustrate the present invention, and are not to be construed as limiting thereof.

EXAMPLE 1 Materials and Methods

Bacterial strains. Wild-type (WT) serovar Typhimurium (ATCC 14028s) and its isogenic fnr mutant (NC 983) were used throughout the studies described herein. The mutant strain was constructed by transducing the fnr::Tn10 mutation from serovar Typhimurium [SL2986/TN 2958 (fnr::Tn10)] to strain 14028s using P22 phage (all from the culture collection of S. Libby). The transductants were plated on Evans blueuranine agar, and the tetracycline marker was eliminated (Bochner et al., (1980) J. Bacteriol. 143:926-933). The Tet^(s) and FNR⁻ phenotypes were confirmed by the inability of NC983 (fnr mutant) to grow on media containing tetracycline (10 μg/ml) and by its inability to grow anaerobically on M9 minimal medium containing glycerol plus nitrate, respectively. Sequence analysis of fnr and neighboring genes (i.e., ogt and ydaA, respectively) in NC 893 showed that the remnant of Tn10 (tnpA) interrupts fnr between bp 106 and 107 and has no polar effect on ogt or ydaA (FIG. 1).

For complementation studies, a low-copy-number plasmid expressing fnr (pfnr) was constructed. The complete fnr sequence starting from the stop codon of ogtA (TGA [indicated in boldface type]) to 21 bp downstream of fnr (i.e., a 972 bp fragment) was amplified from WT strain 14028s with the following primers: fnr-Forward, 5′-ATATCCATGGTGAATATACAGGAAAAAGTGC-3′ (an NcoI site is underlined; SEQ ID NO:1); fnr-Reverse, 5′-ATATATTCAGCTGCATCAATGGTTTAGCTGACG-3′ (a PvuII site is underlined; SEQ ID NO:2). The PCR product was digested with Ncol and PvuII and ligated into the low-copy-number vector pACYC184 cut with NcoI and PvuII. Thus, in the new plasmid (pfnr) the Cmr gene in pACYC184 is replaced with the fnr gene. The plasmid (pfnr) was electroporated and maintained in E. coli DH5α. Transformants were confirmed for Tet^(r) (15 μg/ml) and Cms (20 μg/ml) on Luria-Bertani (LB) plates, and the presence of the fnr gene was confirmed by restriction analysis using EcoRI and HindIII. The plasmid isolated from DH5α was used to complement the fnr mutant. Transformants were selected on LB plates containing tetracycline (15 μg/ml).

Growth conditions. The WT and the fnr mutant were grown anaerobically at 37° C. in MOPS (morpholinepropanesulfonic acid)-buffered (100 mM, pH 7.4) LB broth supplemented with 20 mM D-xylose (LB-MOPS-X). This medium was used in order to avoid the indirect effects of pH and catabolite repression. A Coy anaerobic chamber (Coy, Ann Arbor, Mich.) and anaerobic gas mixture (10% H2, 5% CO₂, and 85% N₂) were used. All solutions were preequilibrated for 48 h in the chamber. Cells from frozen stocks were used to inoculate LB-MOPS-X broth. Cultures were grown for 16 h and used to inoculate fresh anoxic media. The anaerobic growth kinetics of the mutant and the WT strains were similar, and the doubling times of the fnr mutant and the WT were 53.9±1.2 and 45.4±2.9 min, respectively.

RNA isolation. Anaerobic cultures were used to inoculate three independent flasks each containing 150 ml of anoxic LB-MOPS-X. The three independent cultures were grown to an optical density at 600 nm (OD600) of 0.25 to 0.35, pooled, and treated with RNAlater (QIAGEN, Valencia, Calif.) to fix the cells and preserve the quality of the RNA. Total RNA was extracted with the Rneasy RNA extraction kit (QIAGEN), and the samples were treated with RNase-free DNase (Invitrogen, Carlsbad, Calif.). The absence of contaminating DNA and the quality of the RNA was confirmed by PCR amplification of known genes and by using agarose gel electrophoresis. Aliquots of the RNA samples were kept at −80° C. for use in the microarray and quantitative real-time reverse transcription-PCR (qRT-PCR) studies.

Microarray studies. Serovar Typhimurium microarray slides were prepared and used as previously described in Porwollik, S. et al., “The delta uvrB mutations in the Ames strains of Salmonella span 15-119 gene” Mutat. Res. 483:1-11 (2001). The SuperScript Indirect cDNA labeling system (Invitrogen) was used to synthesize the cDNA for the hybridizations. Each experiment consisted of two hybridizations, on two slides, and was carried out in Corning Hybridization Chambers at 42° C. overnight. Dye swapping was performed to avoid dye-associated effects on cDNA synthesis. The slides were washed at increasing stringencies (2×SSC [1×SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 0.1% sodium dodecyl sulfate [SDS], 42° C.; 0.1% SSC, 0.1% SDS, room temperature; 0.1% SSC, room temperature). Following hybridization, the microarrays were scanned for the Cy3 and Cy5 fluorescent signals with a ScanArray 4000 microarray scanner from GSI Lumonics (Watertown, Mass.). The intensity of every spot was codified as the sum of the intensities of all the pixels within a circle positioned over the spot itself and the background as the sum of the intensities of an identical number of pixels in the immediate surroundings of the circled spot.

Data analysis. Cy3 and Cy5 values for each spot were normalized over the total intensity for each dye to account for differences in total intensity between the two scanned images. The consistency of the data obtained from the microarray analysis was evaluated by two methods: (i) a pair-wise comparison, calculated with a two-tailed Student's t test and analyzed by the MEAN and TTEST procedures of SAS-STAT statistical software (SAS Institute, Cary, N.C.) (the effective degrees of freedom for the t test were calculated as described previously in Satterthwaite, F. E. “An approximate distribution of estimates of variance components” Biometrics Bull. 2:110-114 (1946)); and (ii) a regularized t test followed by a posterior probability of differential expression [PPDE (p)] method. These statistical analyses are implemented in the Cyber-T software package available online at the website of the Institute for Genomics and Bioinformatics of the University of California, Irvine. The signal intensity at each spot from the FNR mutant and the WT were background subtracted, normalized, and used to calculate the ratio of gene expression between the two strains. All replicas were combined, and the median expression ratios and standard deviations were calculated for open reading frames (ORFs) showing ≧2.5-fold change.

qRT-PCR. qRT-PCR was used to validate the microarray data, where 19 genes were randomly chosen from the differentially expressed genes. This technique was also used to confirm the expression of a set of selected genes. qRT-PCRs were carried out with the QuantiTect SYBR green RT-PCR kit (QIAGEN) and an iCycler (Bio-Rad, Hercules, Calif.), and the data were analyzed by the Bio-Rad Optical System software, version 3.1, according to manufacturer specifications. To ensure accurate quantification of the mRNA levels, three amplifications for each gene were made with 1:5:25 dilutions of the total RNA. Measured mRNA levels were normalized to the mRNA levels of the housekeeping gene rpoD (σ70). Normalized values were used to calculate the ratios of the expression levels in the fnr mutant relative to the WT.

Logo graph and promoter analysis. The information matrix for the generation of the FNR logo was produced by using the alignment of the E. coli FNR binding sequences, available at http://arep.med.harvard.edu/ecoli_matrices/. The alignment of the FNR motifs from this website did not include the motifs present in the sodA and mutM promoters; therefore, they were included in our analysis. To account for differences in nucleotide usage or slight variations in consensus sequences, a second alignment was built for serovar Typhimurium using the 5′ regions of the homologous genes originally used to build the E. coli information matrix. The alignment was used to prepare a new information matrix using the Patser software (version 3d), available at http://rsat.ub.ac.be/rsat/. A graphical representation (FIG. 2) of the matrices through a logo graph was obtained with Weblogo software (version 2.8.1, 18 Oct. 2004), available at http://weblogo.berkeley.edu/.

Motility assay and electron microscopy. The motilities of the WT, the fnr mutant, and the complemented mutant/pfnr were evaluated under anoxic conditions. Ten microliters of anaerobically grown (16 h) cells were spotted onto LB-MOPS-X agar (0.6% agar) plates and incubated at 37° C. for 24 h. The diameter of the growth halo was used as a measure of motility. Scanning electron microscopy (SEM) was used to examine the morphology of the extracellular surfaces. WT and fnr cultures were grown anaerobically (OD600, 0.3 to 0.4) and centrifuged, and the pellets were resuspended in a fixative solution (3% glutaraldehyde in 0.1 M phosphate-buffered saline [PBS] [pH 7.4]) under anaerobic conditions. The fixed samples were rinsed in 0.1 M PBS buffer, postfixed with 1% osmium tetroxide in 0.1 M PBS for 2 h, and rinsed with PBS, all at 4° C. An aliquot of each sample was filtered through a 0.1-μm filter. Each filter was dehydrated through a graded ethanol series (up to 100%), brought to room temperature, critical point dried with liquid CO₂ (Tousimis Research, Rockville, Md.), placed on stubs, and sputter coated with Au/Pd (Anatech Ltd., Denver, N.C.). Samples were viewed at 15 kV with a JEOL 5900LV SEM (JEOL USA, Peabody, Mass.). Transmission electron microscopy (TEM) and negative staining were used to visualize the flagella. WT and fnr cultures were grown anaerobically (OD600, 0.3 to 0.4), and a 20-μl aliquot of each sample was separately placed on a Formvar-carbon grid. The grids were washed with 0.1 M sodium acetate (pH 6.6), negatively stained with 2% phosphotungstic acid (PTA), and air dried for 5 min before being viewed at 80 kV with a JEOL JEM-100S TEM (JEOL USA, Peabody, Mass.).

Pathocenicity assays. Immunocompetent 6- to 8-week-old C57BL/6 mice and their congenic iNOS−/− and pg91phox^(−/−) immunodeficient mice (bred in the University of Colorado Health Science Center [UCHSC] animal facility according to Institutional Animal Care and Use Committee guidelines) were used in this study. Stationary-phase serovar Typhimurium (WT and fnr mutant) cultures grown aerobically in LB-MOPS-X broth were used, and the cells were diluted in PBS. For oral (p.o.) challenge, groups of 10 mice were gavaged with 5×10⁶ or 5×10⁷ CFU in 200 μl of PBS/mouse. For intraperitoneal (i.p.) challenge, groups of five mice were inoculated with 250 CFU in 500 μl of PBS/mouse. Mortality was scored over a 15- to 30-day period.

Macrophage assay. Peritoneal macrophages were harvested from C57BL/6 mice and pg91phox^(−/−) immunodeficient mice (bred in the UCHSC animal facility) 4 days after intraperitoneal inoculation with 1 mg/ml sodium periodate and used as previously described in DeGroote, M. A. et al. “Periplasmic superoxide dismutase protects Salmonella from products of phagocyte NADPH-oxidase and nitric oxide synthase” Proc. Natl. Acad. Sci. 94:13997-14001 (1997). Macrophages were challenged (multiplicity of infection of 2) for 25 min with the different test strains. Stationary-phase cultures grown aerobically in LB-MOPS-X broth were used as outlined above. Prior to infection, each strain was opsonized with 10% normal mouse serum for 20 min. After the challenge, extracellular bacteria were removed from the monolayers by washing with prewarmed RPMI medium (Cellgro, Herndon, Va.) containing gentamicin (6 mg/ml) (Sigma), the Salmonella-infected macrophages were lysed at indicated time points, and the surviving bacteria were enumerated on LB agar plates. The results are expressed as percent survival relative to the number of viable intracellular bacteria recovered at time zero (i.e., after washing and removal of the extracellular bacteria, 25 min after infection).

Microarray data. The microarray data are accessible via GEO accession number GSE3657 at http://www.ncbi.nlm.nih.gov/qeo (the disclosure of which is incorporated herein by reference in its entirety).

EXAMPLE 2 Transcriptome Profiling

Out of 4,579 genes, the two-tailed Student t test produced a set of 1,664 coding sequences showing significant differences (P<0.05) between the fnr mutant and the WT. The analysis was restricted to include highly affected genes (i.e., having a ratio of ≧2.5-fold). Under this constraint, 311 genes were differentially expressed in the fnr mutant relative to the WT; of these, 189 genes were up-regulated and 122 genes were down-regulated by FNR (Table 3). The 311 FNR-regulated genes were classified into clusters of orthologous groups (COGs) as defined at http://www.ncbi.nlm.nih.gov/COG. Throughout the study levels of transcription in the fnr mutant were compared to that in the WT strain. Thus, genes repressed by FNR possess values of >1, while genes activated by FNR have values of <1.

In order to globally validate the microarray data, 19 of the 311 differentially expressed genes for qRT-PCR were selected. The measured levels of mRNA were normalized to the mRNA levels of the housekeeping gene rpoD. The specific priers used for qRT-PCR and the normalized mRNA levels are shown in Table 1. The microarray and qRT-PCR data were log₂ transformed and plotted (FIG. 3). The correlation between the two sets of data was 0.94 (P<0.05).

To determine whether a binding site for FNR might be present in the region upstream of the candidate FNR-regulated genes, 5′ regions of these genes were searched for the presence of a putative FNR-binding motif using a Salmonella logo graph (FIG. 2). One hundred ten out of the 189 genes activated by FNR (58%) and 59 out of the 122 genes repressed by FNR (48%) contained at least one putative FNR-binding site.

EXAMPLE 3 FNR as a Repressor

Transcription of the genes required for aerobic metabolism, energy generation, and nitric oxide detoxification was repressed by FNR. In particular, the genes coding for cytochrome c oxidase (cyoABCDE), cytochrome cd complex (cydAB), NADH-dehydrogenase (nuoBCEFJLN), succinyl-coenzyme A (CoA) metabolism (sucBCD), fumarases (fumB, stm0761, and stm0762), and the NO.-detoxifying flavohemoglobin (hmpA) were expressed at higher levels in the fnr mutant than in the WT (Table 3). Also, genes required for L-lactate metabolism (IId-PRD) and for the production of phosphoenolpyruvate (pykF), oxaloacetate (ppc), and acetoacetyl-CoA (yqeF) were expressed at higher levels in the mutant than in the WT (Table 3).

EXAMPLE 4 FNR as an Activator

Several genes associated with anaerobic metabolism, flagellar biosynthesis, motility, chemotaxis, and Salmonella pathogenesis were activated by FNR. The genes constituting the dms operon, dmsABC (encoding the anaerobic dimethyl sulfoxide reductase), required for the use of dimethyl sulfoxide (DMSO) as an anaerobic electron acceptor, had the lowest expression levels (i.e., −200-, −62-, and −23-fold, respectively) in the fnr mutant relative to the WT (Table 3). Two other operons coding for putative anaerobic DMSO reductases (STM4305 to STM4307 and STM2528 to STM2530) were also under positive control by FNR. The genes required for the conversion of pyruvate to phosphoenolpyruvate (pps), Ac-CoA (aceF), Ac-P (pta), and OAc (ackA), as well as those for the production of formate (tdcE, yfiD, focA) and D-lactate (IdhA), were expressed at lower levels in the fnr mutant than in the WT. In addition, the genes coding for a universal stress protein (ynaF), a ferritinlike protein (ftnB), an ATP-dependent helicase (hrpA), and aerotaxis/redox sensing (aer) were also positively regulated by FNR (Table 3).

The genes for ethanolamine utilization (eut operon) had lower transcript levels in the fnr mutant (FIG. 4B). Although the FNR-dependent genes for tetrathionate utilization (ttrABCSR), a major anaerobic electron acceptor, were not affected by the lack of FNR, this was not surprising since tetrathionate is also needed to induce expression.

Several of the middle flagellar (class 2) genes (e.g., flgNMDEFGKL and fliZADSTHJLM) and late flagellar (class 3) genes (e.g., cheZYBRMWA, motBA, aer, trg, and tsr) had lower transcript levels in the fnr mutant than in the WT (FIG. 4C to E). There was no significant difference in the transcript levels of the early flagellar genes (class 1) flhD and flhc, whose gene products FlhD/FlhC are the master regulators of flagellar biosynthesis (FIG. 4D). In addition, many newly identified flagellar genes (i.e., mcpA, mcpC, and cheV) had lower expression levels in the fnr mutant, while the expression of mcpB was not affected.

Several genes in SPI-1 (e.g., prgKJIH, iagB, sicA, spaPO, invJICBAEGF) had lower levels of expression in the fnr mutant than in the WT (FIG. 4A). This region contains genes coding for a type three secretion system and for proteins required for invasion and interaction with host cells. The data also show that genes belonging to the other SPIs were unaffected by the lack of FNR. However, the virulence operon srfABC, which is located outside SPI-2 and regulated by a two-component regulatory system (SsrAB) located on SPI-2 (Waterman et al. (2003) Cell. Microbiol. 5:501-511; Worley et al., (2000) Mol. Microbiol. 36:749-761), was differentially regulated by FNR. The effects of FNR on a subset of the above-mentioned invasion and virulence genes were further confirmed by measuring the levels of mRNA in the fnr mutant and the WT strains by qRT-PCR (Table 2).

EXAMPLE 5 Effects of FNR on Motility and Flagella

Expression of the flagellar biosynthesis, motility, and chemotaxis genes was lower in the fnr mutant than in the WT. Therefore, the WT, fnr mutant was compared to the mutant cells harboring pfnr for motility in soft agar under anaerobic conditions. The data indicate that the fnr mutant was nonmotile and that the lack of motility was complemented (˜75%) by the inclusion of pfnr. The 100% complementation by pfnr is probably due to extra copies of the global regulator FNR. The WT was also compared to the mutant for the presence of flagella by SEM and TEM. Taken together, these data show that the fnr mutant is nonmotile due to the lack of flagella.

EXAMPLE 6 Effects of FNR on Pathogenicity and Killing by Macrophages

FNR positively regulates the expression of various loci (see Table 3), such as motility and SPI-1 genes that are important determinants for Salmonella pathogenesis, so the virulence of fnr in a murine model of mucosal and acute infection was tested. In immunocompetent C57BL/6 mice, the fnr mutant was completely attenuated over a 15-day period following an oral challenge with 5×10⁶ or 5×10⁷ CFU/mouse, while the WT strain killed all mice within 10 or 12 days, respectively (FIG. 5A). The mutant strain was also 100% attenuated when 250 CFU/mouse were inoculated i.p. (FIG. 5B). The different Salmonella strains were also tested for the ability to survive killing by macrophages (FIG. 6). Similar numbers of fnr mutant and WT cells were recovered from the macrophages 25 min after infection (designated as time zero postinfection). Data in FIG. 6A indicate that the lack of FNR resulted in a dramatic reduction in the ability of Salmonella to replicate in macrophages. Interestingly, most of the killing of the WT by macrophages took place during the first 2 h postinfection (i.e., the WT resisted further killing beyond 2 h), while the viability of the fnr mutant continued to decline by 1 log between 2 and 20 h postinfection (FIGS. 6A and B). Data in FIG. 6B also show that this phenotype is complemented in fnr mutant cells harboring pfnr. Congenic iNOS−/− mice (unable to make NO.) and pg91phox^(−/−) mice (defective in oxidative burst oxidase) were used to examine the roles of reactive nitrogen and oxygen species (RNS and ROS), respectively, in resistance to an acute systemic infection with FNR-deficient or WT Salmonella. The fnr mutant was as attenuated in iNOS^(−/−) mice as in congenic WT C57BL/6 controls. In sharp contrast, the fnr mutant killed pg91phox^(−/−) mice, albeit at a lower rate than the WT strain (FIGS. 7A and B). Consistent with the in vivo data, the WT and the isogenic fnr mutant survived to similar extents in NADPH oxidase-deficient macrophages isolated from pg91phox^(−/−) mice (FIG. 7C).

The foregoing is illustrative of the present invention, and is not to be construed as limiting thereof. The invention is defined by the following claims, with equivalents of the claims to be included therein. TABLE 1 Validation of microarray data using qRT-PCR of randomly selected genes relative to the housekeeping gene, rpoD^(a). Ratio of SEQ Frag- fnr mutant/WT Log₂ ratio ID ment S. Typhimurium qRT- Micro- qRT- Micro- Locus^(b) Name^(c) Primer sequence^(d) NO: (bp)^(e) Gene Function^(f) PCR^(g) array^(h) PCR^(i) array^(j) STM3217 aer CGTACAACATCTTAATCGTAGC 3 163 Aerotaxis sensor recep- 0.190 0.210 −2.4 −2.3 TTCGTTCAGATCATTATTACCC tor; senses cellular redox state or proton motive force STM1781 cheM GCCAATTTCAAAAATATGACG 5 114 Methyl-accepting chemo- 0.036 0.120 −4.8 −3.1 GTCCAGAAACTGAATAAGTTCG 6 taxis protein II; aspartate sensor- receptor STM0441 cyoC TATTTAGCTCCATTACCTACGG 7 134 Cytochrome o ubiquinol 153.967 7.096 7.3 2.8 GGAATTCATAGAGTTCCATCC 8 oxidase subunit III STM1803 dadA TAACCTTTCGCTTTAATACTCC 9 156 D-Amino acid dehydro- 2.835 3.169 1.5 1.7 GATATCAACAATGCCTTTAAGC 10 genase subunit STM0964 dmsA AGCGTCTTATCAAAGAGTATGG 11 154 Anaerobic dimethyl 0.001 0.005 −9.8 −7.6 TCACCGTAGTGATTAAGATAACC 12 sulfoxide reductase, subunit A STM2892 invJ TTGCTATCGTCTAAAAATAGGC 13 128 Surface presentation of 0.246 0.182 −2.0 −2.5 TTGATATTATCGTCAGAGATTCC 14 antigens; secretory proteins STM2324 nuoF GGATATCGAGACACTTGAGC 15 163 NADH dehydrogenase I, 2.894 2.600 1.5 1.4 GATTAAATGGGTATTACTGAACG 16 chain F STM0650 STM0650 CAACAGCTTATTGATTTAGTGG 17 130 Putative hydrolase, C 0.476 0.219 −1.1 −2.2 CTAACGATTTTTCTTCAATGG 18 terminus STM2787 STM2787 AAGCGAATACAGCTATGAACC 19 144 Tricarboxylic transport 28.241 6.892 4.8 2.8 ATTAGCTTTTGCAGAACATGG 20 STM4463 STM4463 AAGGTATCAGCCAGTCTACG 21 142 Putative arginine 0.325 0.181 −1.6 −2.5 CGTATGGATAAGGATAAATTCG 22 repressor STM4535 STM4535 TAAGCCAGCAGGTAGATACG 23 139 Putative PTS permease 6.053 8.217 2.6 3.0 CGACATAAAGAGATCGATAACC 24 STM2464 eutN AGGACAAATCGTATGTACCG 25 153 Putative detox protein 0.062 0.125 −4.0 −3.0 ACCAGCAGTACCCACTCTCC 26 in ethanolamine utili- zation STM2454 eutR GGTAAAAGAGCAGCATAAAGC 27 118 Putative regulator; 0.043 0.195 −4.6 −2.4 ATTATCACTCAAGACCTTACGC 28 ethanolamine operon (AraC/XylS family) STM2470 eutS AATAAAGAACGCATTATTCAGG 29 137 Putative carboxysome 0.049 0.073 −4.3 −3.8 GTTAAAGTCATAATGCCAATCG 30 structural protein; ethanol utilization STM1172 flgM AGCGACATTAATATGGAACG 31 126 Anti-FliA (anti-sigma) 0.050 0.174 −4.3 −2.5 TTTACTCTGTAAGTAGCTCTGC 32 factor; also known as RflB protein STM3692 lldP TGATTAAACTCAAGCTGAAAGG 33 189 LctP transporter; L- 76.492 16.003 6.3 4.0 CCGAAATTTTATAGACAAAGACC 34 lactate permease STM3693 lldR GAACAGAATATCGTGCAACC 35 153 Putative transcriptional 68.378 30.597 6.1 4.9 GAGTCTGATTTTCTCTTTGTCG 36 regulator for lct operon (GntR family) STM1923 motA GGTTATCGGTACAGTTTTCG 37 194 Proton conductor com- 0.048 0.092 −4.4 −3.4 TAGATTTTGTGTATTTCGAACG 38 ponent of motor; torque generator STM4277 nrfA GACTAACTCTCTGTCGAAAACC 39 159 Nitrite reductase; peri- 0.051 0.324 −4.3 −1.6 ATTTTATGGTCGGTGTAGAGC 40 plasmic cytochrome c₅₅₂ ^(a)STM3211 (rpoD) was used as the reference gene where no significant change in expression level was observed. The primer sequences (5′ to 3′) used for rpoD were as follows: CGATGTCTCTGAAGAAGTGC (forward; SEQ ID NO:41) and TTCAACCATCTCTTTCTTCG (reverse; SEQ ID NO:42). The size of the fragment generated is 150 bp. ^(b)Location of the open reading frame (ORF) in the S. Typhimurium LT2 genome. ^(c)Respective gene name or symbol. ^(d)For each set, the first primer is the forward primer and the second primer is the reverse primer. ^(e)Size of the amplified PCR product. ^(f)Functional classification according to the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. ^(g)Expression levels of quantitative reverse transcriptase polymerase chain reaction - values shown as the ratio between the fnr mutant and the wild-type; where values <1 indicate that FNR acts as an activator, and values >1 indicate FNR acts as a repressor. ^(h)Expression levels from the microarray data - values shown as the ratio between the fnr mutant and the wild-type; where values <1 indicate that FNR acts as an activator, and values >1 indicate FNR acts as a repressor. ^(i)Expression levels of quantitative reverse transcriptase polymerase chain reaction comparing the fnr mutant versus the wild-type - shown in signal to log2 ratio (SLR). ^(j)Expression levels of microarray data comparing the fnr mutant versus the wild-type - shown in signal to 10g2 ratio (SLR).

TABLE 2 qRT-PCR of Selected Invasion and Virulence Genes^(a) Frag- SEQ ment ID size Locus^(b) Name^(c) Primer sequence^(d) NO: (bp)^(e) Ratio^(f) STM2893 invI 5′-CTTCGCTATCAGGATGAGG-3′ 43 161 −9.27 5′-CGAACAATAGACTGCTTACG-3′ 44 STM2874 prgH 5′-GGCTCGTCAGGTTTTAGC-3′ 45 190 −8.45 5′-CTTGCTCATCGTGTTTCG-3′ 46 STM2871 prgK 5′-ATTCGCTGGTATCGTCTCC-3′ 47 199 −8.56 5′-GAACCTCGTTCATATACGG-3′ 48 STM2886 sicA 5′-GATTACACCATGGGACTGG-3′ 49 207 −3.92 5′-CAGAGACTCATCTTCAGTACG-3′ 50 STM1593 srfA 5′-AGGCGGCATTTAGTCAGG-3′ 51 176 −4.33 5′-GACAGGTAAGCTCCACAGC-3′ 52 STM1594 srfB 5′-GGTACCAGAAATACAGATGG-3′ 53 190 −6.55 5′-GCCGATATCAATCGATGC-3′ 54 ^(a)dSTM3211 (rpoD) was used as the reference gene where no significant change in expression level was observed. The primer sequences used for rpoD were as follows: 5′-CGATGTCTCTGAAGAAGTGC-3′ (forward; SEQ ID NO:41) and 5′-TTCAACCATCTCTTTCTTCG-3′ (reverse; SEQ ID NO:42). The size of the fragment generated was 150 bp. ^(b)Location of the open reading frame (ORF) in the S. Typhimurium LT2 genome. ^(c)Respective gene name or symbol. ^(d)For each set, the first primer is the forward and the second primer is the reverse. ^(e)Size of the amplified PCR product. ^(f)Ratio of the transcription levels in the fnr mutant relative to the wild-type.

TABLE 3 Differentially expressed genes and the presence/absence of putative FNR-binding motifs in their 5′ regions. STM Gene t Prob In Locus^(a) Category^(b) Name^(c) Function^(d) value^(e) DF^(f) t^(g) Ratio^(h) Strand^(i) Start^(j) End^(k) Sequence^(l) Score^(m) (P)^(n) PSLT018 — pefA plasmid- −6.11 5.92 9.16E − 04 −2.56 encoded fimbriae; subunit major fimbrial subunit PSLT019 — pefB plasmid- −9.86 6.59 346E − 05 −4.59 R −337 −316 tttcTTTTTTGATATATGTCTTTTCAtgta 5.41 −7.58 encoded fimbriae; regulation STM0002 E thrA aspartokinase −11.82 7.27 5.20E − 06 −3.33 R −351 −330 GGAATTGGTTGAAAATAAATATatcg 5.71 −7.83 I, bifunc- tional enxyme N- terminal is aspartokinaseI and C-terminal is homoserine dehydrogenase I STM0041 G STM0041 putative −9.21 5.78 1.15E − 04 −3.19 glycosyl hydrolase STM0042 G STM0042 putative −12.79 5.16 4.17E − 05 −3.32 sodium galactoside symporter STM0153 C aceF pyruvate −7.07 5.72 4.93E − 04 −3.83 D −52 −31 gaatAATGGCTATCGAAATCAAAGTAccgg 4.98 −7.24 dehydrogenase, dihydrolipoyl- transacetylase component STM0178 G yadI putative PTS −6.35 5.43 1.05E − 03 −7.00 D −263 −242 tttaTAATATATATTTAATCAATTATtttg 5.19 −7.41 enzyme STM0439 H cyoE protohaeme IX 9.48 5.20 1.77E − 04 7.71 D −102 −81 tctgGATTATGTGGAACCTCAACTACaaca 4.54 −6.9 farnesyl- transferase (haeme O biosynthesis STM0440 C cyoD cytochrome o 13.11 5.21 3.45E − 05 7.05 R −326 −305 tatcGGGATGGAACTCTATGAATTCCatca 4.64 −6.98 ubiquinol oxidase sub- unit IV STM0441 C cyoC cytochrome o 36.33 5.46 9.96E − 08 7.10 ubiquinol oxidase sub- unit III STM0442 C cyoB cytochrome o 22.84 5.64 8.89E − 07 5.05 R −206 −185 aaccTGATTTGTTCAAGGACGTTATTaaca 4.18 −6.63 ubiquinol oxidase sub- unit I STM0443 C cyoA cytochrome o 22.81 5.46 1.25E − 06 4.51 D −68 −47 ccgtGGAATTGAGGTCGTTAAATGAGactc 5.84 −7.94 ubiquinol oxidase sub- unit II STM0465 S ybaY glycoprotein/ −15.14 5.29 1.46E − 05 −4.75 R −75 −54 ctggTGCATTGATGATAAGGAGAATTgaat 5.34 −7.53 polysaccharide metabolism STM0467 — ffs signal −9.58 5.21 1.67E − 04 −4.45 recognition particle, RNA component STM0650 G STM0650 putative −9.87 5.46 1.10E − 04 −4.56 D −55 −34 aaggGAAAATGATTATGAGCAATGAGactt 6.95 −8.95 hydrolase C- terminus STM0659 O hscC putative −15.49 8.16 2.46E − 07 −2.82 R −128 −107 gcgtGACATTGATAAAGATCACCACGccag 5.25 −7.46 heatshock protein, homolog of hsp70 in Hsc66 sub- family STM0662 E gltL ABC 12.96 5.46 2.61E − 05 4.39 R −309 −288 actgGCAGTCGATGAAGCTCATTATTctgc 5.97 −8.06 superfamily (atpbind), glutamate/ aspartate transporter STM0663 E gltK ABC 12.08 8.19 1.67E − 06 2.81 superfamily (membrane), glutamate/ aspartate transporter STM0664 E gltJ ABC 12.47 7.16 4.09E − 06 2.67 D −62 −41 tttcGGAGTAGATGTATGTCAATAGActgg 4.58 −6.93 superfamily (membrane), glutamate/ aspartate transporter STM0665 E gltI ABC 10.65 5.77 5.20E − 05 4.24 D −216 −195 taggATTTTTGCCTCTGAACGGTGCGgcgc 5.67 −7.6 superfamily (bindprot), glutamate/ aspartate transporter STM0699 R STM0699 putative −15.11 6.35 3.25E − 06 −4.22 R −30 −9 ggaaGTCACTGATATAGCAGAAATACtggc 6.99 −8.99 cytoplasmic protein STM0728 L nei endonuclease 16.01 6.47 190E − 06 2.57 D −80 −59 tccaTTAATCAACTGTTAACAAAGGAtatt 5.12 −7.35 VIII removing oxidized pyrimidines may also remove oxidized purines in absence of MutY and Fpg [EC:3.2.-.-] STM0737 C sucB 2-oxoglutarate 14.92 9.44 7.01E − 08 2.75 dehydrogenase (dihydrolipoyl- transsuccinase E2 component) STM0738 C sucC succinyl-CoA 21.50 5.79 9.65E − 07 4.03 D −39 −18 acatGAATATCAGGCAAAACAACTTTttgc 6.69 −8.71 synthetase, beta subunit STM0739 C sucD succinyl-CoA 23.03 5.62 8.87E − 07 4.66 synthetase, alpha subunit STM0740 C cydA cytochrome d 17.22 6.09 2.13E − 06 2.55 R −307 −286 gccaTAAATTGATCGCTGTCGAAAAAagca 10.38 −13.11 terminal oxidase, polypeptide subunit I [EC:1.10.3.-] STM0741 C cydB cytochrome d 21.16 5.67 1.30E − 06 3.74 D −169 −148 cagaATTGTTCCTGATGTTCAAATTTgcac 5.62 −7.76 terminal oxidase polypeptide subunit II STM0742 S ybgT putative outer 11.38 7.56 5.01E − 06 4.34 R −165 −144 tgttCGTACCGATCATTCTGATCTACacca 4.83 −7.12 membrane lipoprotein STM0743 S ybgE putative inner 13.92 9.36 1.44E − 07 3.48 R −102 −81 cacgTGCACTGTTGGAAGAGGTTATCcgac 4.31 −6.72 membrane lipoprotein STM0759 — ybgS putative −14.35 5.04 2.80E − 05 −4.60 homeobox protein STM0761 C STM0761 fumarate 6.55 5.53 8.38E − 04 4.48 hydratase Class I anaerobic STM0762 C STM0762 fumarate 8.26 5.15 3.67E − 04 5.69 D −340 −319 agttTATTTTTCTTTCTATCAAATAAtgtc 6.33 −8.37 hydratase, alpha subunit STM0781 P modA ABC −22.42 7.26 5.78E − 08 −3.12 R −140 −119 tttaATCGTTAATGGGTATGAATAACcgct 6.43 −8.47 superfamily (periperm), molybdate transporter STM0790 — hutU pseudogene; 9.49 5.45 1.36E − 04 5.44 frameshift relative to Pseudomonas putida urocanate hydratase (HUTU) SW:P25080 STM0791 E hutH histidine 19.06 6.84 3.51E − 07 4.55 ammonia lyase STM0828 E glnQ ABC 8.23 6.06 1.66E − 04 2.86 superfamily (atpbind), glutamine high- affinity transporter STM0830 E glnH ABC 9.60 5.47 1.26E − 04 3.70 superfamily (bindprot), glutamine high- affinity transporter STM0853 — yliH putative −15.57 6.53 2.08E − 06 −3.33 cytoplasmic protein STM0907 R aSTM09097 Fels-1 −6.72 5.39 8.16E − 04 −3.12 prophage; putative chitinase STM0912 O aSTM0912 Fels-1 11.94 7.50 3.81E − 06 3.40 prophage; protease subunits of ATP-dependent proteases, ClpP family STM0964 C dmsA anaerobic −18.73 5.00 7.95E − 06 −200.85 D −151 −130 ctacTTTTTCGATATATATCAGACTTtata 7.44 −9.43 dimethyl sulfoxide reductase, subunit A STM0965 C dmsB anaerobic −53.46 5.29 1.93E − 08 −62.55 dimethyl sulfoxide reductase, subunit B STM0966 R dmsC anaerobic −28.93 5.04 8.52E − 07 −23.60 R −260 −239 gtaaGAAACCGATTTGCGTCGAATCCtgcc 8.79 −10.93 dimethyl sulfoxide reductase, subunit C STM0972 — STM0972 homologous 5.62 6.48 1.04E − 03 3.07 D −256 −235 aataATTCTCAACATAATTCAGATGTgtcc 4.68 −7 01 to secreted protein sopD STM0974 P focA putative FNT −7.49 5.77 3.53E − 04 −3.19 R −129 −108 ggcgAGATATGATCTATATCAAATTCtcat 8.35 −10.41 family, formate transporter (formate channel 1) STM0989 — STM0989 mukF protein −10.99 5.11 9.47E − 05 −4.90 R −279 −258 cgtgCGCGCTGAAATGCGTTAACATGatcc 4 −65 (killing factor KicB) STM1118 — yccJ putative −9.37 5.50 1.38E − 04 −4.94 cytoplasmic protein STM1119 R wraB trp-repressor −10.54 5.13 1.14E − 04 −6.45 D −167 −146 attaATTATTGTTATAAATCAAAGAAatgg 9.3 −11.57 binding protein STM1123 S STM1123 putative 4.28 6.28 4.69E − 03 3.13 periplasmic protein STM1124 — putA bifunctional 24.50 6.20 2.07E − 07 7.57 in plasma membrane proline dehydrogenase and pyrroline- 5-carboxylate dehydrogenase OR in cyto- plasma tran- scriptional repressor STM1125 E putP SSS family, 14.50 5.46 1.44E − 05 7.16 D −195 −174 tgtaAATGGTGTGTTAAATCGATTGTgaat 7.78 −9.79 major sodium/ proline symporter STM1126 — phoH PhoB- 9.41 6.88 3.56E − 05 2.63 NA NA NA NA NA NA dependent, ATP-binding pho regulon component STM1128 E STM1128 putative −18.20 6.39 9.58E − 07 −4.78 R −289 −268 cctgAAGCCTGTTTGAACGCAATATCggat 5.25 −7.45 sodium/ glucose cotransporter STM1129 G STM1129 putative −15.72 5.52 8.59E − 06 −6.50 inner membrane protein STM1130 S STM1130 putative −9.85 5.15 1.56E − 04 −11.85 inner membrane protein STM1131 — STM1131 putative −10.50 5.84 5.25E − 05 −4.67 D −58 −37 cggaGTATTTTATGAAAATCAACAAAtatc 7.06 −9.06 outer membrane protein STM1132 G STM1132 putative −9.42 5.29 1.67E − 04 −6.20 R −120 −99 ttcgGCAATTGATATGACTTAAAAATtaat 10.03 −12.57 sugar transort protein STM1133 R STM1133 putative −14.98 5.29 1.56E − 05 −5.56 D −90 −69 cgtgAAAGTTTTCAATCAACAAAAGAattt 4.6 −6.94 dehydrogenases and related proteins STM1138 — ycdZ putative −9.09 5.03 2.62E − 04 −11.00 D −106 −85 agaaTAATGTGATGTAAATCACCCTTaact 5.45 −7.62 inner membrane protein STM1171 N flgN flagellar −12.69 5.24 3.93E − 05 −7.85 biosynthesis: belived to be export chaperone for FlgK and FlgL STM1172 K flgM anti-FliA −13.69 5.30 2.46E − 05 5.75 R −72 −51 cgtaACCCTCGATGAGGATAAATAAAtgag 5.44 −7.61 (anti-sigma) factor; also known as RflB protein STM1176 N flgD flagellar −11.76 5.49 4.21E − 05 −2.94 biosynthesis, initiation of hook assembly STM1177 N flgE flagellar −14.54 5.88 7.83E − 06 −3.56 biosynthesis, hook protein STM1178 N flgF flagellar −7.59 6.06 2.58E − 04 −2.81 biosynthesis, cell-proximal portion of basal-body rod STM1179 N flgG flagellar −7.52 5.56 4.10E − 04 −3.50 biosynthesis, cell-distal portion of basal-body rod STM1183 N flgK flagellar −11.80 5.20 5.95E − 05 −5.67 biosynthesis, hook-filament junction protein 1 STM1184 N flgL flagellar −11.04 5.33 7.16E − 05 −4.18 biosynthesis; hook-filament junction protein STM1227 E pepT putative −13.20 6.24 8.57E − 06 −2.67 peptidase T(aminotri- peptidase) STM1254 — STM1254 putative −8.06 5.65 2.64E − 04 −3.82 outer membrane lipoprotein STM1271 P yeaR putative 13.89 5.66 1.37E − 05 4.25 R −284 −263 gcaaTTCTTTGATTGGCCTTCTTTTCgtcg 4.81 −7.1 cytoplasmic protein STM1272 — yoaG putative 6.92 7.98 1.23E − 04 2.87 D −225 −204 cggaAGAGATCATGGTGATCAATGCCggcg 8.55 −10.65 cytoplasmic protein STM1300 — STM1300 putative −8.78 5.08 2.93E − 04 −4.83 D −256 −235 ggttGTATTTGCGTTTTATCAGAATAtgta 6.36 −8.4 periplasmic protein STM1301 L STM1301 putative −9.26 5.65 1.27E − 04 −3.36 mutator MutT protein STM1349 G pps phospho- −19.01 5.69 2.28E − 06 −3.45 D −58 −37 aggaTTGTTCGATGTCCAACAATGGCtcgt 5.74 −7.86 enolpyruvate synthase STM1378 G pykF pyruvate 14.46 5.51 1.36E − 05 2.55 kinase I (formerly F), fructose stimulated STM1489 H ynfK putative −11.20 5.23 7.52E − 05 −8.40 R −140 −119 aactCAAGCTGATTGCCCTTGCCATAtctt 4.73 −7.04 dethiobiotin synthase STM1498 C STM1498 putative −21.41 5.10 3.44E − 06 −27.55 R −177 −156 atacAAATCTGGTGGAAATCGAAAAAatct 4.87 −7.15 dimethyl sulphoxide reductase STM1499 C STM1499 putative −19.08 5.35 3.98E − 06 −8.27 D −101 −80 ataaTTTCGTTATAGTTATCAATATAtagc 4.38 −6.78 dimethyl sulphoxide reductase, chain A1 STM1509 — ydfZ putative −14.41 5.58 1.25E − 05 −7.62 R −161 −140 ccgtGAGCTTGATCAAAAACAAAAAAaatt 8.84 −10.98 cytoplasmic protein STM1538 C STM1538 putative 11.55 5.78 3.28E − 05 3.96 hydrogenase-1 large subunit STM1539 C STM1539 putative 8.66 5.44 2.21E − 04 3.53 hydrogenase small subunit STM1562 — STM1562 putative −11.30 5.28 6.68E − 05 −4.99 D −217 −196 tgctTTATTCATCAAACATCAAAATCagtc 6.71 −8.73 periplasmic transport protein STM1564 — yddX putative −10.75 8.27 3.83E − 06 −2.93 cytoplasmic protein STM1568 C fdnI formate −28.97 6.32 5.81E − 08 −3.98 R −119 −98 tcgcCGGTCTGATTTACCACTACATCggta 7.14 −9.14 dehydro- genase-N cytochrome B556(Fdn) gamma sub- unit, nitrate- inducible STM1569 C fdnH formate −9.33 8.93 6.68E − 06 −2.50 dehydro- genase, iron-sulfur subunit (formate dehydro- genase beta sub- unit) [EC:1.2.1.2] STM1593 — srfA ssrAB −5.82 6.28 9.63E − 04 −2.52 D −185 −164 acccTGATTTAACTTACGTCAAGTGGaaac 5.8 −7.91 activated gene STM1594 S srfB ssrAB −14.70 6.14 5.14E − 06 −2.88 D −58 −37 tgccTGATTTTATGTTGGTCAATCTGtgtg 5.31 −7.5 activated gene STM1626 N trg methyl- −13.30 5.46 2.28E − 05 5.72 accepting chemotaxis protein III, ribose and galactose sensor receptor STM1640 S ydcF putative −11.44 5.63 4.15E − 05 −5.72 inner membrane protein STMI641 L hrpA helicase, −21.19 6.25 4.68E − 07 −20.97 R −217 −196 gtgcCCCGTTGCTTGTTGACACTTTAttca 4.72 −7.04 ATP- dependent STM1642 I acpD acyl carrier −11.32 7.81 4.05E − 06 −4.01 D −107 −86 tgaaTAAAGTGTCAACAAGCAACGGGgcac 4.72 −7.04 protein phospho- diesterase STM1647 C ldhA fermentative −16.29 5.95 3.65E − 06 −24.42 D −139 −118 tcatTATATGTATGACTATCAATTATtttt 5.05 −7.29 D-lactate dehydrogenase, NAD-dependent STM1648 O hslJ heat shock −8.34 5.41 2.75E − 04 −5.00 R −74 −53 ttaaCTATCAGATTACAGAGAATATCaatg 4.11 −6.57 protein hslJ STM1650 — STM1650 putative −5.38 7.56 7.97E − 04 −3.52 reverse transcriptase STM1651 C nifJ putative −8.67 6.43 8.87E − 05 −4.97 pyruvate- flavodoxin oxidore- ductase STM1652 T ynaF putative −20.67 5.01 4.81E − 06 −116.15 R −282 −261 ttatTGAATTAAACGGTAACATCTCtttt 4.7 −7.02 universal stress protein STM1653 P STM1653 putative −10.25 5.85 5.92E − 05 −6.56 membrane transporter of cations STM1657 N STM1657 putative −9.41 6.29 6.15E − 05 −4.01 D −52 −31 caaaAATGTTGAGAAATATCAGCGTCagga 8.58 −10.68 methyl- accepting chemotaxis protein STM1658 S ydaL putative −28.29 6.75 2.87E − 08 −4.01 Smr domain STM1659 L ogt O-6- −6.79 6.25 4.20E − 04 −2.92 alkylguanine- DNA/cysteine- protein methyl- transferase STM1660 — fnr transcrip- −8.24 5.04 4.11E − 04 −6.55 D −88 −67 tgttAAAATTGACAAATATCAATTACggct 11.43 −14.93 tional regulation of aerobic, anaerobic respiration, osmotic balance (CRP family) STM1688 K pspC phage shock 11.96 6.86 7.63E − 06 3.23 R −45 −24 gggtGGAATCAATCTGAATAAAAAACtatg 6.11 −8.16 protein; regulatory gene, activates expression of psp operon with PspB STM1706 J yciH putative 9.58 5.71 9.91E − 05 4.32 translation initiation factor SUI1 STM1732 M ompW outer −6.72 5.07 1.05E − 03 −8.36 R −172 −151 gttcTAAATTAATCTGGATCAATAAAtgtt 8.33 −10.39 membrane protein W; colicin S4 receptor; putative transporter STM1746 — oppA ABC 16.43 6.25 2.23E − 06 3.83 R −290 −269 atttCACATTGTTGATAAGTATTTTCattt 5.36 −7.54 superfamily (periplasm), oligopeptide transport protein with chaperone properties STM1767 T narL response 11.78 6.53 1.22E − 05 2.78 regulator in two-component regulatory system with NarX (or NarQ), regulates anaerobic respiration and fermentation (LuxR/UhpA familiy) STM1781 P ychM putative −10.77 6.07 3.49E − 05 −3.33 R −2.30 −209 acgaAGAATCGATTTCCGCCATGTTCgagc 5.29 −7.49 SulP family transport protein STM1795 E STM1795 putative 12.42 5.46 3.28E − 05 5.33 R −302 −281 acatAACATTGATACATGTCGTTATCataa 6.57 −8.6 homologue of glutamic dehyrogenase STM1798 — ycgR putative −14.17 5.94 8.40E − 06 −4.09 D −267 −246 tggcGATAACGCCGGCAATCAAACCAaaaa 6.66 −8.68 inner membrane protein STM1803 E dadA D-amino 10.10 8.96 3.40E − 06 3.16 R −261 −240 cctcCACATTGAACGGCAAAAAATCGggta 4.58 −6.92 acid dehydrogenase subunit STM1831 G manY Sugar 15.20 5.98 5.28E − 06 3.73 R −146 −125 atccGAAACTGAAAATGATGGATTTAattg 4.99 −7.24 Specific PTS family, mannose- specific enzyme IIC STM1832 G manZ Sugar 14.15 9.24 1.42E − 07 2.96 D −277 −256 ttggTTATGCGATGGTTATCAATATGatgc 7.21 −9.2 Specific PTS family, mannose- specific enzyme IID STM1915 N cheZ chemotactic −9.59 5.76 9.42E − 05 −3.56 response; CheY protein phophatase STM1916 T cheY chemotaxis −9.32 5.69 1.18E − 04 −3.74 D −111 −90 agcaGATGTTGGCGAAAATCAGTGCCggac 8.6 −10.7 regulator, transmits chemoreceptor signals to flagelllar motor components STM1917 N cheB methyl −8.37 5.74 2.00E − 04 −4.33 esterase, response regulator for chemotaxis (cheA sensor) STM1918 N cheR glutamate −22.41 8.99 3.40E − 09 −3.32 methyl- transferase, response regulator for chemotaxis STM1919 N cheM methyl −18.86 5.13 6.12E − 06 −8.31 accepting chemotaxis protein II, aspartate sensor- receptor STM1920 N cheW purine- −14.43 5.32 1.82E − 05 −4.31 D −296 −275 gggcATTGTTGTGATCCTGCAAAGCGcggg 4.39 −6.78 binding chemotaxis protein; regulation STM1921 N cheA sensory −16.27 6.02 3.32E − 06 −4.67 D −39 −18 ggatATTAGCGATTTTTATCAGACATtttt 4.84 −7.12 histitine protein kinase, transduces signal between chemo- signal receptors and CheB and CheY STM1922 N motB enables −15.03 5.33 1.43E − 05 −7.00 R −177 −156 atgcGCCGCCGATTGCCGTGGAATTTggtc 5.72 −7.84 flagellar motor rotation, linking torque machinery to cell wall STM1923 N motA proton −5.97 5.07 1.80E − 03 −10.82 conductor component of motor, torque generator STM1932 P ftnB ferritin- −21.51 5.01 3.92E − 06 −21.11 D −95 −74 tctcGTCTGTCATGCACATCAACACTttct 4.24 −6.67 like protein STM1955 — fliZ putative −15.76 5.35 109E − 05 −6.25 D −331 −310 acagGAAAACCCGTTACATCAACTGCtgga 5.78 −7.9 regulator of FliA STM1956 K fliA sigma F −21.86 8.81 5.60E − 09 −5.96 R −64 −43 acgcAGGGCTGTTTATCGTGAATTCActgt 4.87 −7.15 (sigma 28) factor of RNA polymerase, transcription of late flagellar genes (class 3a and 3b operons) STM1960 N fliD flagellar −15.69 6.81 1.35E − 06 −4.45 R −82 −61 cttaACTACTGTTTGCAATCAAAAAGgaag 4.63 −6.97 biosynthesis; filament capping protein; enables filament assembly STM1961 O fliS flagellar −9.80 5.27 1.40E − 04 −5.10 R −231 −210 acgcCACGCTGAAAAGCCTGACAAAAcagt 4.08 −6.56 biosynthesis; repressor of class 3a and 3b operons (RflA activity STM1962 — fliT flagellar −7.66 5.16 5.25E − 04 −6.03 biosynthesis; possible export chaperone for FliD STM1971 N fliH flagellar −8.61 6.32 1.01E − 04 −2.94 biosynthesis; possible export of flagellar proteins STM1973 N fliJ flagellar −7.71 6.36 1.88E − 04 −4.27 fliJ protein STM1975 N fliL flagellar −8.94 5.55 1.68E − 04 −2.79 biosynthesis STM1976 N fliM flagellar −9.19 5.26 1.95E − 04 −3.07 R −161 −140 aacaAAAACTGATTGCCGCCATTAAAgaga 5.62 −7.76 biosynthesis, component of motor switch and energizing STM1978 N fliO flagellar −5.21 6.02 1.98E − 03 −2.76 biosynthesis STM2059 S yeeX putative 8.96 6.90 4.79E − 05 2.75 cytoplasmic protein STM2183 F cdd cytidine/ −17.85 5.47 4.66E − 06 −7.71 R −157 −136 atttTTCATTGAAGTTTCACAAGTTGcata 5.31 −7.51 deoxycytidine deaminase STM2186 E STM2186 putative −15.60 5.64 7.43E − 06 −4.18 D −269 −248 cttcTTTTTTATCGTTAATCTATTTAttat 5.46 −7.63 NADPH- dependent glutamate synthase beta chain or related oxidoreductase STM2187 F yeiA putative −15.69 5.44 9.74E − 06 −4.05 dihydro- pyrimidine dehydrogenase STM2277 F nrdA ribonucleoside 26.74 5.26 8.07E − 07 11.15 D −60 −39 ggtaGAAAACCACATGAATCAGAGTCtgct 4.2 −6.64 diphosphate reductase 1, alpha subunit STM2278 F nrdB ribonucleoside 29.51 5.69 1.92E − 07 9.57 D −68 −47 tcccATAAAGGATTCACTTCAATGGCatac 6.02 −8.11 diphosphate reductase 1 beta subunit STM2279 C yfaE putative 6.33 5.30 1.17E − 03 3.37 R −297 −276 acggTTCGATGATCGGCCTGAATAAAgata 5.02 −7.27 ferredoxin STM2280 G STM2280 putative 11.04 6.42 2.06E − 05 4.32 permease STM2287 — STM2287 putative 4.59 6.33 3.24E − 03 3.46 R −279 −258 ggggATAACTGAATATCCCCAATAATaatt 4.46 −6.84 cytoplasmic protein STM2314 T STM2314 putative −25.76 5.48 6.21E − 07 −6.99 chemotaxis signal transduction protein STM2315 R yfbK putative von −15.60 9.01 7.88E − 08 −2.84 Willebrand factor, vWF type A domain STM2316 — nuoN NADH 8.29 6.13 1.50E − 04 2.67 R −334 −313 tggtGCCGGTGATTACCGTGATCTCCacct 4.26 −6.69 dehydrogenase I chain N STM2318 C nuoL NADH 8.02 7.14 8.05E − 05 2.54 R −261 −240 tgttTATGCTGATTGGGCTGGAAATCatga 5.57 −7.71 dehydrogenase I chain L STM2320 C nuoJ NADH 11.27 6.55 1.58E − 05 2.54 dehydrogenase I chain J [EC:1.6.5.3] STM2324 C nuoF NADH 9.85 7.93 1.01E − 05 2.60 dehydrogenase I chain F STM2325 C nuoE NADH 8.07 8.32 3.23E − 05 2.65 dehydrogenase I chain E STM2326 C nuoC NADH 22.56 6.50 2.04E − 07 3.34 dehydrogenase I chain C, D STM2327 C nuoB NADH 11.71 6.20 1.86E − 05 2.52 dehydrogenase I chain B [EC:1.6.5.3] STM2334 R yfbT putative 18.20 6.34 1.03E − 06 3.49 R −76 −55 gagcGCGAATGAAATCAATCAAATCAttaa 5.55 −7.7 phosphatase STM2335 S yfbU putative 6.74 5.61 6.87E − 04 3.39 cytoplasmic protein STM2337 C ackA acetate −16.97 6.34 1.60E − 06 −3.51 R −147 −126 tcctGCGCATGATGTTAATCATAAATgtca 4.76 −7.07 kinase A (propionate kinase 2) STM2338 C pta phosphotran- −6.43 5.94 6.96E − 04 −3.17 sacetylase STM2340 G STM2340 putative 11.33 5.19 7.42E − 05 6.60 D −82 −61 gctcAATGAGGCCATTCATCAACTGGaggt 4.18 −6.62 transketolase STM2341 G STM2341 putative 23.38 5.42 1.19E − 06 6.47 transketolase STM2342 S STM2342 putative 9.98 5.52 9.77E − 05 5.22 R −276 −255 aaaaAGTATTAAAGAAACTCAATATTgacg 6.82 −8.83 inner membrane protein STM2343 G STM2343 putative 10.35 6.09 4.30E − 05 3.34 D −64 −43 tttaAAAGGTGACAATAATGAAAATCatgg 4.64 −6.97 cytoplasmic protein STM2409 F nupC NUP family, −15.30 5.45 1.09E − 05 −3.91 D −347 −326 gtttATTGATAATGATTATCAAGTGCattt 5.87 −7.97 nucleoside transport STM2454 K eutR putative −12.08 5.35 4.34E − 05 −5.13 regulator ethanolamine operon (AraC/XylS family) STM2455 Q eutK putative −9.27 5.21 1.97E − 04 −6.77 D −61 −40 aacgGAGGCTGCCAATGATCAATGCCctgg 4.45 −6.83 carboxysome structural protein, ethanolamine utilization STM2456 E eutL putative −9.22 5.22 1.99E − 04 −6.68 carboxysome structural protein, ethanolamine utilization STM2457 E eutC ethanolamine −16.21 5.56 6.85E − 06 −7.07 ammonia-lyase, light chain STM2458 E eutB ethanolamine −17.30 5.54 4.94E − 06 −6.33 D −315 −294 ccgcATTACTCACGGTCATCAACGCGctga 5.38 −7.56 ammonia-lyase, heavy chain STM2459 E eutA CPPZ-55 −19.26 5.16 5.24E − 06 −6.17 prophage; chaperonin in ethanola- mine utili- zation STM2460 E eutH putative −17.75 5.32 6.09E − 06 −6.29 transport protein, ethanolamine utilization STM2462 E eutJ paral putative −7.74 5.05 5.52E − 04 −7.30 heatshock protein (Hsp70) STM2463 C eutE putative −18.52 5.34 4.73E − 06 −7.02 R −64 −43 aaatAGGATTGAACATCATGAATCAAcagg 4.88 −7.15 aldehyde oxidoreductase in ethanolamine utilization STM2464 Q eutN putative −14.11 5.14 2.65E − 05 −8.00 D −194 −173 tggaAGAAGTGTTCCCGATCAGCTTCaaag 5.21 −7.42 detox protein in ethanolamine utilization STM2465 Q eutM putative −28.26 5.11 8.21E − 07 −11.02 R −250 −229 ctatCGCGCTGTTGGGCCGCTAATTCaggg 4.58 −6.93 detox protein in ethanolamine utilization STM2466 C eutD putative −15.83 5.11 1.53E − 05 −10.36 phosphotran- sacetylase in ethanolamine utilization STM2467 E eutT putative −16.88 5.92 3.13E − 06 −6.59 R −237 −216 cgtgGACGCTGAACTACGACGAAATCgaca 6.89 −8.9 cobalamin adenosyl- transferase, ethanolamine utilization STM2468 E eutQ putative −18.58 5.26 5.33E − 06 −7.60 ethanolamine utilization protein STM2469 E eutP putative −20.06 5.13 4.47E − 06 −9.38 R −247 −226 aaacGGCGATGATCGCTGGCGATTTAgcga 4.71 −7.03 ethanolamine utilization protein STM2470 E eutS putative −10.43 5.05 1.32E − 04 −13.70 R −154 −133 ttctCTTAGTGATCTACCTCACCTTTtaca 5.95 −8.05 carboxysome structural protein, ethanol utilization STM2479 E aegA putative −7.82 7.39 7.90E − 05 −3.37 R −187 −166 gaaaTAAATTGATCTGCCACAGGTTCtgga 7.26 −9.26 oxidoreductase STM2530 C STM2530 putative −10 14 7.00 1.96E − 05 −3.67 D −158 −137 ttatGAATTTCATTTAATTTAAAGTTaatg 6.79 −8.8 anaerobic dimethyl- sulfoxide reductase STM2556 C hmpA dihydro- 15.99 5.95 4.09E − 06 3.01 R −95 −74 agatGCATTTGATATACATCATTAGAtttt 6.24 −8.3 pteridine reductase 2 and nitric oxide dioxygenase activity STM2558 E cadB ABC family, −6.95 5.19 1.01E − 03 −6.43 D −219 −198 tatgTTAATTCAAAAAAATCAATCTAtcag 6.78 −8.8 lysine/ cadaverine transport protein STM2559 E cadA lysine −10.67 5.18 1.02E − 04 −5.58 R −221 −200 tcgtCAGTCTGATCATCCTGATGTTCtacg 5.74 −7.86 decarboxy- lase 1 STM2646 R yfiD putative −26.43 5.69 3.54E − 07 −5.08 D −179 −158 ggttTTTATTGATTTAAATCAAAGAAtgaa 10.76 −13.71 formate acetyltrans- ferase STM2733 — STM2733 Fels-2 −5.44 8.92 4.26E − 04 −2.72 prophage: similar to E. coli retron Ec67 STM2786 S STM2786 tricarboxylic 19.84 5.84 1.38E − 06 8.21 transport STM2787 — STM2787 tricarboxylic 10.54 9.96 1.01E − 06 6.89 transport STM2788 S STM2788 tricarboxylic 11.85 5.46 4.19E − 05 3.46 R −107 −86 ttgaCCGGCTGCTTGATGTCACCTTAcctc 4.26 −6.68 transport STM2795 S ygaU putative −3.59 5.59 1.31E − 02 −2.98 D −55 −34 aggtGAATATGGGACTTTTCAATTTTgtaa 5.43 −7.6 LysM domain STM2851 C hycC hydrogenase −5.41 8.55 5.07E − 04 −3.49 3, membrane subunit (part of FHL complex) STM2855 O hypB hydrogenase-3 −14.31 6.06 6.74E − 06 −3.12 R −143 −122 cataGAGATTGATGAAACTGAAGATTaatg 9.23 −11.47 accessory protein, assembly of metallocenter STM2856 O hypC putative −9.09 6.18 8.40E − 05 −2.56 hydrogenase expression/ formation protein STM2857 O hypD putative −8.01 5.29 3.76E − 04 −2.97 hydrogenase expression/ formation protein STM2871 U prgK cell −15.27 7.06 1.15E − 06 −3.25 invasion protein; lipoprotein, may link inner and outer membranes STM2872 — prgJ cell −9.60 5.35 1.43E − 04 −4.65 R −344 −323 agccCACTTTAATTTAACGTAAATAAggaa 5.69 −7.82 invasion protein; cytoplasmic STM2873 — prgI cell −12.42 5.80 2.13E − 05 −4.16 R −83 −62 agccCACTTTAATTTAACGTAAATAAggaa 5.69 −7.82 invasion protein; cytoplasmic STM2874 — prgH cell −16.99 6.31 1.65E − 06 −3.85 invasion protein STM2877 M iagB cell −4.52 5.49 5.01E − 03 −3.55 R −86 −65 ccgcTTGATTAAATTACGGTAAAATCtgag 4.68 −7 invasion protein STM2886 R sicA surface −10.24 5.19 1.24E − 04 −2.80 D −57 −36 ggagTAAGTAATGGATTATCAAAATAatgt 4.34 −6.75 presentation of antigens; secretory proteins STM2890 U spaP surface −5.39 5.53 2.17E − 03 −4.27 D −88 −67 cttaGGCGTTGAGATCCATGAATGGCtgag 4.61 −6.95 presentation of antigens; secretory proteins STM2891 N spaO surface −8.43 5.86 1.72E − 04 −3.67 presentation of antigens; secretory proteins STM2892 — invJ surface −7.06 5.22 7.34E − 04 −5.51 D −239 −218 tttaGAACTCCAGATTATACAAATTCagga 4.22 −6.66 presentation of antigens; secretory proteins STM2893 — invI surface −12.02 5.46 3.91E − 05 −4.44 R −190 −169 gcttTTCATTGACTTGGGAGAATATCgtcc 6.09 −8.16 presentation of antigens; secretory proteins STM2894 N invC surface −6.62 6.04 5.54E − 04 −2.79 presentation of antigens; secretory proteins STM2895 — invB surface −10.44 5.50 7.85E − 05 −3.88 R −267 −246 ccgcTAATTTGATGGATCTCATTACActta 8.41 −10.48 presentation of antigens; secretory proteins STM2896 U invA invasion −6.84 5.81 5.50E − 04 −3.34 protein STM2897 — invE invasion −5.52 6.12 1.40E − 03 −3.09 R −29 −8 tccgGTATTTCATTTTCCAGAATATTgtcc 4.35 −6.76 protein STM2898 N invG invasion −6.82 5.89 5.30E − 04 −3.48 D −126 −105 cacaTTTTTCTAGTGAGATCAAAGAGctga 7.49 −9.49 protein; outer membrane STM2899 K invF invasion −5.45 5.63 1.95E − 03 −3.57 protein STM2983 — ygdI putative −7.97 6.00 2.09E − 04 −3.64 lipoprotein STM3019 I yqeF putative 10.03 6.84 2.46E − 05 2.58 R −249 −228 ctatTGATTTGCTGTGGAACAAGAAAacgc 4.54 −6.9 acetyl-CoA acetyl- transferase STM3131 S STM3131 putative −17.74 9.67 1.07E − 08 −7.24 R −77 −56 actgCCACCTGATCAACAAGGAGATAaatc 5.09 −7.32 cytoplasmic protein STM3136 G STM3136 putative D- 9.94 5.61 8.96E − 05 2.88 mannonate oxidoreductase STM3138 N STM3138 putative −8.98 5.43 1.84E − 04 −4.76 methyl- accepting chemotaxis protein STM3155 — STM3155 putative −7.23 7.42 1.31E − 04 −2.81 R −78 −57 gtatACCACTGATCGTAAAGGATATTtagt 7.28 −9.28 cytoplasmic protein STM3216 N STM316 putative −15.35 7.19 9.30E − 07 −3.37 R −280 −259 tctaCCTATTAATAGGTATAAACTCAgtta 5.59 −7.73 methyl- accepting chemotaxis protein STM3217 T aer aerotaxis −12.23 5.32 4.29E − 05 −4.77 D −238 −217 aaagGTTGTCCACGCTAAACAATTTCataa 8.02 −10.04 sensor receptor, senses cellular redox state or proton motive force STM3225 E ygjU putative 17.69 9.71 1.04E − 08 3.68 dicarboxylate permease STM3238 S yhaN putative −6.92 6.10 4.20E − 04 −3.18 R −146 −125 aaggCGCTTCGTTGTACCTGATTATTatta 4.55 −6.9 inner membrane protein STM3240 E tdcG L-serine −16.72 5.57 5.68E − 06 −4.80 R −249 −228 ggatGCGATTGAACATCCGGAAAACTaccc 6.02 −8.11 deaminase STM3241 C tdcE pyruvate −9.34 10.00 2.95E − 06 −2.66 formate- lyase 4/2- ketobutyrate formate- lyase STM3242 C tdcD propionate −14.83 7.09 1.35E − 06 −4.10 R −147 −126 tgacCATCCTGAATATTGTCTACAAAttgt 4.53 −6.89 kinase/ acetate kinase II, anaerobic STM3245 K tdcA transcrip- −17.03 5.41 6.59E − 06 −6.04 D −239 −218 cctgTTTTTTGATTGAAATCAGGCTAagtt 8.48 −10.57 tional activator of tdc operon (LysR family) STM3248 I garR tartronate 15.78 5.93 4.53E − 06 4.16 semialdehyde reductase (TSAR) STM3273 I yhbT putative −9.33 5.49 1.43E − 04 −2.71 D −237 −216 acgcAAAATTGTTAACGAACAGGGATttta 5.52 −7.68 lipid carrier protein STM3274 O yhbU putative −10.06 5.51 9.38E − 05 −10.68 R −103 −82 taaaATCCCTGTTCGTTAACAATTTTgcgt 5.52 −7.68 protease STM3275 — yhbV putative −13.35 5.95 1.16E − 05 −10.88 protease STM3334 F STM3334 putative −8.46 6.65 8.47E − 05 −2.58 D −277 −256 agtgATTATTGCCGACTATCTGTTGAaccg 4 −6.5 cytosine deaminase STM3338 G nanT MFS family, −19.92 5.67 1.83E − 06 −3.02 sialic acid transport protein STM3545 R yhhX putative 14.13 5.91 8.84E − 06 3.21 oxidoreductase STM3547 — STM3547 putative 54.21 5.60 7.77E − 09 6.06 transcrip- tional regulator of sugar metabolism STM3548 — STM3548 putative 40.36 5.24 9.82E − 08 9.29 R −327 −306 gcttGCTTATGATGGCACACAATTCAtcta 4.98 −7.24 cytoplasmic protein STM3549 S STM3549 putative 13.96 5.28 2.25E − 05 7.22 inner membrane protein STM3550 R STM3550 putative 22.45 5.17 2.34E − 06 7.40 phospho- triesterase STM3576 P zntA P-type 9.90 5.54 9.92E − 05 2.55 R −261 −240 cgacGCTGCTGTTCATCGGCAATATCgtct 5.02 −7.27 ATPase family, Pb/Cd/Zn/Hg transporting ATPase [EC:3.6.3.33.6.3.5] STM3577 N tcp methyl- −22.22 5.71 9.23E − 07 −5.64 R −126 −105 agcgTGATTTGATGTAAGGTTAATTTttat 6.53 −8.56 accepting transmembrane citrate/phenol chemoreceptor STM3598 E STM3598 putative L- −8.27 6.47 1.13E − 04 −3.70 asparaginase STM3599 R STM3599 putative −7.19 5.11 7.38E − 04 −9.14 D −108 −87 cacaATAGGTTACGTCCCTCAATGTAaagc 4.29 −6.71 inner membrane protein STM3600 G STM3600 putative −9.76 5.07 1.77E − 04 −12.63 R −322 −301 aacgCGCGTTAAACTTCCTGAAAAAAtatg 5 −7.25 sugar kinases, ribokinase family STM3601 M STM3601 putative −26.75 5.09 1.12E − 06 −11.94 R −266 −245 cgcaACAGTTGATTGTCGGCGATAAAatac 7.59 −9.59 phosphosugar isomerase STM3611 T yhjH putative −16.54 5.11 1.23E − 05 −7.89 Diguanylate cyclase/ phospho- diesterase domain 3 STM3626 E dppF ABC 9.03 5.90 1.14E − 04 5.86 superfamily (atp_bind), dipeptide transport protein STM3627 E dppD ABC 8.88 5.24 2.36E − 04 7.65 D −45 −24 ggcgTTATTAAATGTAGATCAATTATcggt 8.18 −10.23 superfamily (atp_bind), dipeptide transport protein STM3628 E dppC ABC 16.86 5.71 4.35E − 06 4.09 superfamily (membrane), dipeptide transport protein 2 STM3629 E dppB ABC 11.76 5.16 6.34E − 05 12.45 D −55 −34 ttcgGGTTATGTTGCAGTTCATTCTCcgac 4.22 −6.66 superfamily (membrane), dipeptide transport protein 1 STM3630 E dppA ABC 9.06 5.06 2.56E − 04 9.90 superfamily (peri_perm), dipeptide transport protein STM3690 — STM3690 putative −15.85 9.97 2.15E − 08 −5.67 R −305 −284 ccgcAAAATTAAATAACATTATCATCcctg 4.96 −7.22 inner membrane lipoprotein STM3692 C lldP LctP 9.84 5.02 1.81E − 04 16.00 D −160 −139 tgtcATTATCCATACACAACAATATTggca 6.37 −8.41 transporter, L-lactate permease STM3693 K lldR putative 12.30 5.04 5.98E − 05 30.60 transcrip- tional regulator for lct operon (GntR family) STM3694 C lldD L-lactate 27.93 5.02 1.05E − 06 28.33 dehydrogenase STM3695 J yibK putative 9.64 9.95 2.31E − 06 2.95 tRNA/rRNA methyl- transferase STM3708 E tdh threonine 7.11 6.53 2.66E − 04 3.16 3-dehydrogenase STM3709 H kbl 2-amino-3- 12.63 6.75 6.02E − 06 2.86 D −298 −277 taacGATATTGCTGCCGATAAAGCCCgcgc 5.12 −7.34 ketobutyrate CoA ligase (glycine acetyl- transferase) STM3750 G yicJ putative −13.67 7.06 2.44E − 06 −2.67 GPH family transport protein STM3801 G dsdX putative 14.70 7.68 6.70E − 07 3.42 R −22 −1 gcacGCTGCTGATCAGCATCGTGTT 5.63 −7.77 Gnt family transport protein STM3802 E dsdA D-serine 17.71 5.05 9.69E − 06 7.90 deaminase (dehydratase) STM3808 — ibpB small heat 6.72 5.53 7.44E − 04 2.85 shock protein STM3820 P STM3820 putative −12.03 6.07 1.83E − 05 −5.87 D −165 −144 tgtaATTATTGATACCAATCAATATCcatg 11 −14.14 cytochrome c peroxidase STM3831 R yidA putative 19.09 7.62 1.03E − 07 4.38 D −220 −199 acggTATTTTCTGTTTGATTAATGAGgtta 7.22 −9.21 hydrolase of the HAD superfamily STM3861 M glmS L-glutamine: 8.04 6.11 1.80E − 04 2.89 R −24 −3 cgcgCAGCGTGATGTAGCTGAAATCCt 4.19 −6.63 D-fructose- 6-phosphate aminotrans- ferase STM3862 M glmU N-acetyl 7.97 5.70 2.67E − 04 2.78 glucosamine- 1-phosphate uridyl- transferase and glucosamine- 1-phosphate acetyl transferase STM3909 E ilvC ketol-acid 10.62 5.70 5.68E − 05 3.38 reductoiso- merase STM4004 H hemN O2-independent 10.06 5.66 8.07E − 05 3.82 copropor- phyrinogen III oxidase STM4007 E glnA glutamine 19.35 5.32 3.91E − 06 5.97 synthetase STM4034 O fdhE putative 9.93 6.01 5.99E − 05 3.12 formate dehydrogenase formation protein ? Mn_fn STM4035 C fdoI formate 8.84 5.80 1.40E − 04 3.60 dehydrogenase, cytochrome B556 (FDO) subunit STM4036 C fdoH formate 21.65 8.93 5.02E − 09 2.85 dehydrogenase- O, Fe-S subunit STM4037 C fdoG formate 7.75 5.52 3.62E − 04 2.73 dehydrogenase STM4062 G pfkA 6-phospho- 12.62 9.16 4.23E − 07 2.97 R −181 −160 cattTGGCCTGACCTGAATCAATTCAgcag 5.19 −7.4 fructokinase I STM4078 G yneB putative 15.91 7.71 3.57E − 07 2.57 R −51 −30 aagaATGGCTGATTTAGATGATATTAaaga 5.53 −7.68 fructose-1, 6-bisphosphate aldolase STM4085 G glpX unknown 6.62 5.50 8.16E − 04 3.20 R −60 −39 ctacGAGTTTGTTATGAGACGAGAACttgc 5.56 −7.71 function in glycerol metabolism STM4109 G talC putative 19.34 8.13 4.38E − 08 4.72 D −221 −200 tcatTATGCTGACGCTTAACAAACACgccg 4.79 −7.09 transaldolase STM4110 G ptsA General PTS 7.39 6.01 3.14E − 04 2.66 D −257 −236 tactGGATTTTTGTAATATCAGTATAaaaa 5.49 −7.65 family, enzyme I STM4113 G frwB PTS system 5.65 5.64 1.62E − 03 2.89 D −83 −62 tttaGATTTTGAGATGAATTAAGCGAggaa 4.79 −7.09 fructose-like IIB component 1 STM4119 C ppc phospho- 9.54 5.26 1.62E − 04 3.40 enolpyruvate carboxylase STM4126 C udhA soluble 13.35 6.46 6.04E − 06 3.17 pyridine nucleotide transhydro- genase STM4229 G malE ABC 56.71 9.34 3.52E − 13 7.00 superfamily (bind_prot) maltose transport protein, substrate recognition for transport and chemotaxis STM4231 G lamB phage lambda 26.26 5.36 7.19E − 07 11.38 receptor protein; maltose high- affinity receptor, facilitates diffusion of maltose and maltoseoligo- saccharides STM4240 S yjbJ putative −6.01 5.16 1.64E − 03 −4.24 cytoplasmic protein STM4277 P nrfA nitrite −7.36 5.12 6.58E − 04 −3.09 R −198 −177 acttACAATTGATTAAAGACAACATTttaa 11.55 −15.16 reductase periplasmic cytochrome c(552) STM4278 — nrfB formate- −7.18 7.31 1.46E − 04 −3.69 D −262 −241 gtttGAATATGCAACAAATCAACGCGgaga 6.12 −8.19 dependent nitrite reductase; a penta- haeme cytochrome c STM4298 G melA alpha- 25.01 5.44 7.96E − 07 7.21 galactosidase STM4299 G melB OPH family, 24.57 5.24 1.29E − 06 6.66 D −327 −306 cgatGATGCAGACCAACATCAACGTGcaaa 4.94 −7.21 melibiose permease II STM4300 C FumB fumarase B 9.38 5.99 8.37E − 05 2.69 R −216 −195 tgccGGGTTTGATTGGCGTGAGCGTCtcct 4.17 −6.62 (fumarate hydratase class I), anaerobic isozyme STM4301 R dcuB Dcu family, 12.46 5.83 2.01E − 05 3.38 R −155 −134 ctggCGCATTGAATATTCGCCATTTCctga 5.55 −7.7 anaerobic C4- dicarboxylate transporter STM4305 — STM4305 putative −15.43 5.16 1.62E − 05 −10.14 anaerobic dimethyl sulfoxide reductase, subunit A STM4306 C STM4306 putative −7.45 5.19 5.86E − 04 −7.59 R −65 −44 cttaAGGAGTGATGTACGATGAAACAgtat 4.33 −6.73 anaerobic dimethyl sulfoxide reductase, subunit B STM4307 R STM4307 putative −13.21 9.88 1.33E − 07 −2.90 anaerobic dimethyl sulfoxide reductase, subunit C STM4308 R STM4308 putative −7.84 6.73 1.27E − 04 −2.55 component of anaerobic dehydrogenases STM4398 E cycA APC family, 13.44 6.79 3.81E − 06 2.54 D −151 −130 gccgATTCTTACCTAATATCGATGAGtcct 5.02 −7.27 D-alanine/ D-serine/ glycine transport protein STM4399 D ytfE putative 7.64 6.16 2.31E − 04 2.96 cell morphogenesis STM4439 C cybC cytochrome 23.97 7.61 1.92E − 08 4.26 R −317 −296 attcTGGGTTGAAAATGGTGAAATCCagta 5.06 −7.3 b(562) STM4452 F nrdD anaerobic −12.74 6.51 7.62E − 06 −3.17 R −304 −283 ttttTACCTTGTTCTACATCAATAAAattg 7.97 −9.99 ribonucleo- side- triphosphate reductase STM4462 — yjgG putative −5.83 5.39 1.64E − 03 −3.63 cytoplasmic protein STM4463 E STM4463 putative −8.53 5.33 2.64E − 04 −5.52 arginine repressor STM4469 E argI ornithine −12.54 9.04 5.08E − 07 −3.36 carbamoyl- transferase 1 STM4510 M STM4510 putative −6.50 5.16 1.14E − 03 −6.35 D −115 −94 gcatTTTTTATATACACATCAAGTTGatag 6.56 −8.61 aspartate racemase STM4511 K yjiE putative −8.28 5.18 3.54E − 04 −6.79 transcrip- tional regulator, LysR family STM4512 — iadA isoaspartyl −16.84 5.28 8.66E − 06 −6.59 R −75 −54 gcagCTTATTGTTTAATAAGGAGTTAtcat 4.52 −6.88 dipeptidase STM4513 S yjiG putative −12.81 5.10 4.53E − 05 −8.61 permease STM4514 — yjiH putative −31.77 6.17 4.45E − 08 −6.56 R −338 −317 gcgtGAAATTGACTAACGTCAAATTTattt 9.1 −11.31 inner membrane protein STM4526 V hsdR endonuclease −10.25 5.85 5.93E − 05 −3.28 R −153 −132 attgTTCGTTGATCACACACAATATGaagt 5.93 −8.02 R, host restriction STM4533 N tsr methyl- −4.07 6.18 6.19E − 03 −2.75 D −301 −280 cgcgTAAAGTTAGGTAAATCAGTGAGtggt 7.31 −9.31 accepting chemotaxis protein I, serine sensor receptor STM4535 G STM4535 putative PTS 18.00 6.01 1.87E − 06 8.22 D −179 −158 agaaCTTATCGAGCAAGATCAACAGTttta 4.23 −6.66 permease STM4536 G STM4536 putative PTS 15.55 5.53 8.94E − 06 4.50 permease STM4537 G STM4537 putative PTS 29.73 6.56 3.04E − 08 6.57 R −172 −151 gttaGCGGATGAAATGACTCAACTTCggga 5.44 −7.61 permease STM4538 G STM4538 putative PTS 12.87 5.17 4.03E − 05 7.25 permease STM4539 M STM4539 putative 7.10 5.07 8.07E − 04 8.20 R −277 −256 cggcCTCCATGATTGATATCACCATTccca 5.1 −7.33 glucosamine- fructose-6- phosphate amino- transferase STM4540 — STM4540 putative 10.51 5.26 9.95E − 05 4.89 glucosamine fructose-6- phosphate amino- transferase STM4561 R osmY hyper- −11.35 5.80 3.54E − 05 −5.19 D −163 −142 tcacGAATGTGATGCCAGTCATTGACttca 4.12 −6.59 osmotically inducible periplasmic protein, RpoS- dependent stationary phase gene STM4565 O yjjW pyruvate −15.96 9.55 3.30E − 08 −3.71 D −34 −13 gcgcTTTAGTCAGTAAGATCATTGCGtttt 5.28 −7.48 formate lyase activating enzyme STM4566 — yjjI putative −20.43 5.09 4.43E − 06 −17.28 R −181 −160 actgTAATGAGATCTGAATCAAATTAtccc 4.68 −7 cytoplasmic protein STM4567 F deoC 2-deoxyribose- −6.83 6.15 4.34E − 04 −2.91 D −184 −163 gggaTAATTTGATTCAGATCTCATTAcagt 4.68 −7 5-phosphate aldolase STM4568 F deoA thymidine −8.83 6.49 7.51E − 05 −2.76 phosphorylase ^(a)Location of the open reading frame (ORF) in the S. Typhimurium LT2 genome. ^(b)Functional category assigned to the gene by the National Center for Biotechnology Information, Cluster of Orthologous Genes (COGs). The designations of functional categories are as follows: C, energy production and conversion, D, cell cycle control and mitosis, E, amino acid metabolism and transport, F, nucleotide metabolism and transport, G, carbohydrate metabolism and transport, H, coenzyme metabolism and transport, I, lipid metabolism and transport, J, translation, K, transcription, L,  #replication, recombination, and repair, M, cell wall/membrane/envelope biogenesis, N, Cell motility, O, post-translational modification, protein turnover, chaperone functions, P, inorganic ion transport and metabolism, Q, secondary metabolites biosynthesis, transport, and catabolism, R, general functional prediction only (typically, prediction of biochemical activity), S, function unknown, T, signal transduction mechanisms, U, intracellular trafficking and secretion, V, defense mechanisms, -, not in COGs. ^(c)Respective gene name or symbol. ^(d)Functional classification according to the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. ^(e)The numerical value of t for the t test (statistical method). ^(f)The degrees of freedom employed for the analysis of each gene. ^(g)The probability associated with the t test for each gene. ^(h)Ratio between the expression level of the fnr mutant relative to the wild-type. ^(i)The strand on which the motif has been localized. R, reverse; D, direct; NA, not available in the Regulatory Sequence Analysis Tools (RSAT) database (the locus identity was not recognized), and a blank cell indicates that no motif was present. ^(j)The starting position of the putative motif. The positions are relative to the region searched and span from −300 to +50 relative to the starting ATG. ^(k)The ending position of the putative motif. The positions are relative to the region searched and span from −300 to +50 relative to the starting ATG. ^(l)The sequence of the HIGHEST RANKING putative motif (capitalized letters) and 4 base pairs (bps) flanking either side of the region (lower case letters). A blank cell indicates that no motif was present. All of the sequences are reported from the 5′ to the 3′ end of the ORF (Open Reading Frame) analyzed. ^(m)The score indicating the similarity of the motif to the information matrix. The cutoff used was a score higher than 4.00 or a In(P) lower than −6.5. ^(n)The natural logarithm of the probability that the putative motif is randomly similar to the information matrix. The cutoff used was a score higher than 4.00 or a In(P) lower than −6.5. 

1. A pharmaceutical composition comprising an attenuated enterobacterium comprising an attenuating mutation in the fnr gene in a pharmaceutically acceptable carrier.
 2. The pharmaceutical composition of claim 1, wherein the attenuating mutation is an attenuating deletion mutation.
 3. The pharmaceutical composition of claim 1, wherein the attenuated enterobacterium is an attenuated Salmonella.
 4. The pharmaceutical composition of claim 3, wherein the attenuated Salmonella is an attenuated S. enterica serovar Typhimurium.
 5. The pharmaceutical composition of claim 1, wherein the attenuated enterobacterium is an attenuated Shigella.
 6. The pharmaceutical composition of claim 1, wherein the attenuated enterobacterium is an attenuated Escherichia coli.
 7. The pharmaceutical composition of claim 6, wherein the attenuated E. coli is an attenuated E. coli strain O157:H7.
 8. An attenuated enterobacterium comprising an attenuating mutation in the fnr gene and a heterologous nucleic acid sequence encoding a foreign antigen.
 9. The attenuated enterobacterium of claim 8, wherein the attenuating mutation is an attenuating deletion mutation.
 10. The attenuated enterobacterium of claim 8, wherein the attenuated enterobacterium is an attenuated Salmonella.
 11. The attenuated enterobacterium of claim 10, wherein the attenuated Salmonella is an attenuated S. enterica serovar Typhimurium.
 12. The attenuated enterobacterium of claim 8, wherein the attenuated enterobacterium is an attenuated Shigella.
 13. The attenuated enterobacterium of claim 8, wherein the attenuated enterobacterium is an attenuated Escherichia coli.
 14. The attenuated enterobacterium of claim 13, wherein the attenuated E. coli is an attenuated E. coli strain O157:H7.
 15. The attenuated enterobacterium of claim 8, wherein the heterologous nucleic acid sequence is incorporated into the bacterial genomic nucleic acid.
 16. The attenuated enterobacterium of claim 9, wherein the heterologous nucleic acid sequence is incorporated into the deleted FNR region.
 17. The attenuated enterobacterium of claim 8, wherein the heterologous nucleic acid sequence is incorporated into a plasmid.
 18. A pharmaceutical composition comprising the attenuated enterobacterium of claim 8 in a pharmaceutically acceptable carrier.
 19. A method of inducing an immune response in a subject comprising administering to the subject an immunogenically effective amount of the pharmaceutical composition of claim
 1. 20. The method of claim 19, wherein an immune response is induced against one or more Salmonella spp.
 21. The method of claim 20, wherein an immune response is induced against S. enterica serovar Typhimurium.
 22. The method of claim 19, wherein an immune response is induced against one or more Shigella spp.
 23. The method of claim 19, wherein an immune response is induced against one or more E. coli spp.
 24. The method of claim 23, wherein an immune response is induced against E. coli strain O157:H7.
 25. A method of inducing an immune response in a subject comprising administering to the subject an immunogenically effective amount of the attenuated enterobacterium of claim
 8. 26. The method of claim 25, wherein the immune response is induced against the foreign antigen and the enterobacterium.
 27. The method of claim 26, wherein an immune response is induced against one or more Salmonella spp.
 28. The method of claim 27, wherein an immune response is induced against S. enterica serovar Typhimurium.
 29. The method of claim 26, wherein an immune response is induced against one or more Shigella spp.
 30. The method of claim 26, wherein an immune response is induced against one or more E. coli spp.
 31. The method of claim 30, wherein an immune response is induced against E. coli strain O157:H7. 